{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example: using a different force field\n",
    "\n",
    "Here we show how to use MDPOW to calculate partition coefficients using an force field that isn't included in the package. To follow along, install `jupyter` in your `mdpow` environment.\n",
    "\n",
    "To implement a new force field, you will need:\n",
    "\n",
    "* `ITP` files for the molecule, the solvents, ions and also the general atom type definitions file (usually just named after the force field itself).\n",
    "* `MDP` files for the energy minimisation, initial relaxation, NPT ensemble run and free energy calculation.\n",
    "* Structure files (`.gro` or `.pdb`) for the solute and non-aqueous solvent. If you are using a type of water that does not come bundled with GROMACS, like in this example, you will also need to create an equilibrated box of pure water.\n",
    "\n",
    "The first thing we'll do is to download the files we need for Martini 3.0."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "from typing import Optional\n",
    "\n",
    "import gromacs\n",
    "import requests as req\n",
    "\n",
    "\n",
    "HERE = Path(\".\")\n",
    "MARTINI_FF = HERE / \"martini.ff\"\n",
    "MARTINI_FF.mkdir(exist_ok=True)\n",
    "\n",
    "MARTINI_ITP = MARTINI_FF / \"forcefield.itp\"\n",
    "MARTINI_IONS = MARTINI_FF / \"martini_v3.0.0_ions_v1.itp\"\n",
    "MARTINI_SMALL_MOLS = MARTINI_FF / \"martini_v3.0.0_small_molecules_v1.itp\"\n",
    "MARTINI_SOLVENTS = MARTINI_FF / \"martini_v3.0.0_solvents_v1.itp\"\n",
    "BENZENE_ITP = MARTINI_SMALL_MOLS\n",
    "\n",
    "MARTINI_WATER = HERE / \"water.gro\"\n",
    "MARTINI_OCTANOL = HERE / \"octanol.gro\"\n",
    "MARTINI_BENZENE = HERE / \"benzene.pdb\"\n",
    "\n",
    "EM_FILE = HERE / \"em.mdp\"\n",
    "EQ_FILE = HERE / \"eq.mdp\"\n",
    "RUN_FILE = HERE / \"run.mdp\"\n",
    "\n",
    "\n",
    "def download_file(\n",
    "    url: str, out: Optional[Path] = None, chunk_size: int = 128, overwrite: bool = False\n",
    "):\n",
    "    \"\"\"Utility function to download files.\"\"\"\n",
    "    if out is None:\n",
    "        out = HERE / Path(url).name\n",
    "\n",
    "    if out.exists() and not overwrite:\n",
    "        return\n",
    "\n",
    "    r = req.get(url, stream=True)\n",
    "    r.raise_for_status()\n",
    "\n",
    "    with out.open(\"wb\") as f:\n",
    "        for chunk in r.iter_content(chunk_size=chunk_size):\n",
    "            f.write(chunk)\n",
    "\n",
    "\n",
    "DOWNLOADS = {\n",
    "    MARTINI_ITP: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0.itp\",\n",
    "    MARTINI_IONS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_ions_v1.itp\",\n",
    "    MARTINI_SMALL_MOLS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_small_molecules_v1.itp\",\n",
    "    MARTINI_SOLVENTS: \"https://raw.githubusercontent.com/marrink-lab/martini-forcefields/main/martini_forcefields/regular/v3.0.0/gmx_files/martini_v3.0.0_solvents_v1.itp\",\n",
    "}\n",
    "\n",
    "for fname, url in DOWNLOADS.items():\n",
    "    download_file(url, fname)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This should have downloaded several files to your workspace.\n",
    "\n",
    "We also need to make a `watermodels.dat` file in the `martini.ff` subdirectory.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "56"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "WATERMODEL_DAT = MARTINI_FF / \"watermodels.dat\"\n",
    "\n",
    "WATERMODEL_DAT.write_text(\"martini-water\\tMARTINI-WATER\\tMartini default water model.\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we set up the files for the Martini 3.0 forcefield."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "from mdpow.forcefields import Forcefield, GromacsSolventModel\n",
    "\n",
    "MARTINI = Forcefield(\n",
    "    \"Martini\",\n",
    "    solvent_models={\n",
    "        \"octanol\": GromacsSolventModel(\n",
    "            identifier=\"octanol\",\n",
    "            itp=MARTINI_SOLVENTS.absolute(),\n",
    "            coordinates=str(MARTINI_OCTANOL.absolute()),\n",
    "            forcefield=\"Martini\",\n",
    "        ),\n",
    "    },\n",
    "    forcefield_dir=MARTINI_FF.absolute(),\n",
    "    ions_itp=MARTINI_IONS.absolute(),\n",
    "    default_water_itp=MARTINI_SOLVENTS.absolute(),\n",
    "    default_water_model=\"martini-water\",\n",
    "    water_models={\n",
    "        \"martini-water\": GromacsSolventModel(\n",
    "            identifier=\"martini-water\",\n",
    "            itp=MARTINI_SOLVENTS.absolute(),\n",
    "            coordinates=str(MARTINI_WATER.absolute()),\n",
    "            forcefield=\"Martini\",\n",
    "        ),\n",
    "    },\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Aqueous simulation\n",
    "\n",
    "We now solvate a benzene molecule in a water box. The first step of this is to set up a `WaterSimulation`, then perform some energy minimisation and create the files needed for relaxation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.equil : INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/water.gro'...\n",
      "                     :-) GROMACS - gmx editconf, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n",
      "Command line:\n",
      "  gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 3.0\n",
      "\n",
      "\n",
      "Back Off! I just backed up boxed.gro to ./#boxed.gro.1#\n",
      "\n",
      "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n",
      "\n",
      "                     :-) GROMACS - gmx solvate, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n",
      "Command line:\n",
      "  gmx solvate -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -cp boxed.gro -cs /home/awsm/MDPOW/doc/examples/martini/water.gro -o solvated.gro\n",
      "\n",
      "Reading solute configuration\n",
      "Reading solvent configuration\n",
      "\n",
      "Initialising inter-atomic distances...\n",
      "Generating solvent configuration\n",
      "Will generate new solvent configuration of 1x1x1 boxes\n",
      "Solvent box contains 1731 atoms in 1731 residues\n",
      "Removed 98 solvent atoms due to solvent-solvent overlap\n",
      "Removed 0 solvent atoms due to solute-solvent overlap\n",
      "Sorting configuration\n",
      "Found 1 molecule type:\n",
      "      W (   1 atoms):  1633 residues\n",
      "Generated solvent containing 1633 atoms in 1633 residues\n",
      "Writing generated configuration to solvated.gro\n",
      "\n",
      "Back Off! I just backed up solvated.gro to ./#solvated.gro.1#\n",
      "\n",
      "Output configuration contains 1636 atoms in 1634 residues\n",
      "Volume                 :     174.316 (nm^3)\n",
      "Density                :     2860.16 (g/l)\n",
      "Number of solvent molecules:   1633   \n",
      "\n",
      "Processing topology\n",
      "\n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#system.top.2#\n",
      "\n",
      "GROMACS reminds you: \"It is a cute toxin.\" (Rebecca Howard)\n",
      "\n",
      "gromacs.setup: INFO     Solvated system with /home/awsm/MDPOW/doc/examples/martini/water.gro\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Note that major changes are planned in future for editconf, to improve usability and utility.\n",
      "Read 3 atoms\n",
      "Volume: 4050 nm^3, corresponds to roughly 1822500 electrons\n",
      "No velocities found\n",
      "    system size :  0.210  0.160  0.248 (nm)\n",
      "    diameter    :  0.270               (nm)\n",
      "    center      :  2.987  0.606  2.315 (nm)\n",
      "    box vectors : 15.000 15.000 18.000 (nm)\n",
      "    box angles  :  90.00  90.00  90.00 (degrees)\n",
      "    box volume  :4050.00               (nm^3)\n",
      "    shift       :  1.716  4.097 -0.098 (nm)\n",
      "new center      :  4.703  4.703  2.217 (nm)\n",
      "new box vectors :  6.270  6.270  6.270 (nm)\n",
      "new box angles  :  60.00  60.00  90.00 (degrees)\n",
      "new box volume  : 174.32               (nm^3)\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "Adding line for 1633 solvent molecules with resname (W) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "gromacs.cbook: INFO     system total charge qtot = 0\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation] After solvation: total charge qtot = 0 = 0\n",
      "gromacs.cbook: INFO     system total charge qtot = 0\n",
      "gromacs.setup: INFO     Building the main index file 'main.ndx'...\n",
      "                     :-) GROMACS - gmx make_ndx, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n",
      "Command line:\n",
      "  gmx make_ndx -f ionized.tpr -o main.ndx\n",
      "\n",
      "\n",
      "Reading structure file\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "\n",
      "Back Off! I just backed up main.ndx to ./#main.ndx.2#\n",
      "\n",
      "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n",
      "\n",
      "                     :-) GROMACS - gmx make_ndx, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n",
      "Command line:\n",
      "  gmx make_ndx -f ionized.tpr -n main.ndx -o main.ndx\n",
      "\n",
      "\n",
      "Reading structure file\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "\n",
      "Back Off! I just backed up main.ndx to ./#main.ndx.3#\n",
      "\n",
      "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n",
      "\n",
      "                     :-) GROMACS - gmx trjconv, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation\n",
      "Command line:\n",
      "  gmx trjconv -ur compact -center -boxcenter tric -pbc mol -f ionized.gro -s ionized.tpr -o compact.pdb -n main.ndx\n",
      "\n",
      "Will write pdb: Protein data bank file\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "Group     0 (         System) has  1636 elements\n",
      "Group     1 (          Other) has  1636 elements\n",
      "Group     2 (           BENZ) has     3 elements\n",
      "Group     3 (              W) has  1633 elements\n",
      "Group     4 (       __main__) has     3 elements\n",
      "Group     5 (__environment__) has  1633 elements\n",
      "Select a group: Group     0 (         System) has  1636 elements\n",
      "Group     1 (          Other) has  1636 elements\n",
      "Group     2 (           BENZ) has     3 elements\n",
      "Group     3 (              W) has  1633 elements\n",
      "Group     4 (       __main__) has     3 elements\n",
      "Group     5 (__environment__) has  1633 elements\n",
      "Select a group: Reading frames from gro file 'This is an auto generated system', 1636 atoms.\n",
      "Reading frame       0 time    0.000   \n",
      "Precision of ionized.gro is 0.001 (nm)\n",
      "\n",
      "Back Off! I just backed up compact.pdb to ./#compact.pdb.1#\n",
      "Last frame          0 time    0.000   \n",
      " ->  frame      0 time    0.000      \n",
      "Last written: frame      0 time    0.000\n",
      "\n",
      "\n",
      "GROMACS reminds you: \"Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia.\" (Roald Hoffmann)\n",
      "\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -f /tmp/tmp_bobqsmz.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -nov\n",
      "\n",
      "\n",
      "NOTE 1 [file /tmp/tmp_bobqsmz.mdp]:\n",
      "  For a correct single-point energy evaluation with nsteps = 0, use\n",
      "  continuation = yes to avoid constraining the input coordinates.\n",
      "\n",
      "\n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/#pp_system.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Note that major changes are planned in future for trjconv, to improve usability and utility.\n",
      "Select group for centering\n",
      "Selected 4: '__main__'\n",
      "Select group for output\n",
      "Selected 0: 'System'\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "(more than 20 non-matching atom names)\n",
      "\n",
      "WARNING 1 [file system.top, line 28]:\n",
      "  999 non-matching atom names\n",
      "  atom names from\n",
      "  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top\n",
      "  will be used\n",
      "  atom names from\n",
      "  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro\n",
      "  will be ignored\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file system.top, line 28]:\n",
      "  For energy conservation with LINCS, lincs_iter should be 2 or larger.\n",
      "\n",
      "\n",
      "Number of degrees of freedom in T-Coupling group rest is 4902.00\n",
      "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n",
      "\n",
      "NOTE 3 [file /tmp/tmp_bobqsmz.mdp]:\n",
      "  NVE simulation with an initial temperature of zero: will use a Verlet\n",
      "  buffer of 10%. Check your energy drift!\n",
      "\n",
      "\n",
      "There were 3 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n",
      "\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top', mdp='em.mdp' ...\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'em.mdp': ['maxwarn', 'pp']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'maxwarn': 1, 'pp': 'processed.top'}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'maxwarn': 1, 'pp': 'processed.top'}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em\n",
      "Command line:\n",
      "  gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -maxwarn 1 -pp processed.top\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -411043105\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "(more than 20 non-matching atom names)\n",
      "Analysing residue names:\n",
      "There are:  1634      Other residues\n",
      "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
      "\n",
      "This run will generate roughly 0 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "(more than 20 non-matching atom names)\n",
      "\n",
      "WARNING 1 [file system.top, line 28]:\n",
      "  999 non-matching atom names\n",
      "  atom names from\n",
      "  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top\n",
      "  will be used\n",
      "  atom names from\n",
      "  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro\n",
      "  will be ignored\n",
      "\n",
      "\n",
      "Number of degrees of freedom in T-Coupling group rest is 4902.00\n",
      "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up em.tpr to ./#em.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Input, output, electricity\" (Joni Mitchell)\n",
      "\n",
      "gromacs.run : WARNING  No 'mdrun_d' binary found so trying 'mdrun' instead.\n",
      "(Note that energy minimization runs better with mdrun_d.)\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/run.py:423: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead.\n",
      "(Note that energy minimization runs better with mdrun_d.)\n",
      "  warnings.warn(wmsg, category=AutoCorrectionWarning)\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em\n",
      "Command line:\n",
      "  gmx mdrun -v -stepout 10 -deffnm em -c em.pdb\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -71328783\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "atom name 638 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 639 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 640 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 641 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 642 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 643 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 644 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 645 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 646 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 647 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 648 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 649 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 650 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 651 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 652 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 653 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 654 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 655 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 656 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "atom name 657 in /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top and /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/solvated.gro does not match (W - W 1)\n",
      "\n",
      "(more than 20 non-matching atom names)\n",
      "Analysing residue names:\n",
      "There are:  1634      Other residues\n",
      "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
      "\n",
      "This run will generate roughly 0 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "Back Off! I just backed up em.log to ./#em.log.1#\n",
      "Reading file em.tpr, VERSION 2023.2 (single precision)\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "\n",
      "Back Off! I just backed up em.trr to ./#em.trr.1#\n",
      "\n",
      "Back Off! I just backed up em.edr to ./#em.edr.1#\n",
      "\n",
      "Steepest Descents:\n",
      "   Tolerance (Fmax)   =  1.00000e+01\n",
      "   Number of steps    =         1000\n",
      "Step=    0, Dmax= 1.0e-02 nm, Epot=  9.59019e+06 Fmax= 1.69656e+07, atom= 149\n",
      "Step=    1, Dmax= 1.0e-02 nm, Epot=  6.21902e+06 Fmax= 6.01139e+06, atom= 478\n",
      "Step=    2, Dmax= 1.2e-02 nm, Epot=  3.58839e+06 Fmax= 2.70774e+06, atom= 17\n",
      "Step=    3, Dmax= 1.4e-02 nm, Epot=  2.18086e+06 Fmax= 1.08770e+06, atom= 1305\n",
      "Step=    4, Dmax= 1.7e-02 nm, Epot=  1.25600e+06 Fmax= 5.29430e+05, atom= 1493\n",
      "Step=    5, Dmax= 2.1e-02 nm, Epot=  7.79933e+05 Fmax= 2.60389e+05, atom= 1513\n",
      "Step=    6, Dmax= 2.5e-02 nm, Epot=  4.76315e+05 Fmax= 1.79135e+05, atom= 1493\n",
      "Step=    7, Dmax= 3.0e-02 nm, Epot=  3.20697e+05 Fmax= 2.25612e+05, atom= 544\n",
      "Step=    8, Dmax= 3.6e-02 nm, Epot=  2.54493e+05 Fmax= 9.11997e+04, atom= 1513\n",
      "Step=    9, Dmax= 4.3e-02 nm, Epot=  1.57693e+05 Fmax= 1.98552e+05, atom= 544\n",
      "Step=   10, Dmax= 5.2e-02 nm, Epot=  1.29573e+05 Fmax= 6.97811e+04, atom= 1043\n",
      "Step=   11, Dmax= 6.2e-02 nm, Epot=  8.43733e+04 Fmax= 2.96448e+05, atom= 200\n",
      "Step=   12, Dmax= 7.4e-02 nm, Epot=  7.16053e+04 Fmax= 2.00453e+04, atom= 200\n",
      "Step=   13, Dmax= 8.9e-02 nm, Epot=  1.52004e+04 Fmax= 5.75859e+04, atom= 200\n",
      "Step=   14, Dmax= 1.1e-01 nm, Epot=  7.52929e+03 Fmax= 2.23154e+04, atom= 200\n",
      "Step=   15, Dmax= 1.3e-01 nm, Epot= -2.26025e+03 Fmax= 3.65146e+04, atom= 1107\n",
      "Step=   16, Dmax= 1.5e-01 nm, Epot= -7.31692e+03 Fmax= 3.23004e+04, atom= 1107\n",
      "Step=   17, Dmax= 1.8e-01 nm, Epot= -8.75253e+03 Fmax= 1.04774e+05, atom= 898\n",
      "Step=   18, Dmax= 2.2e-01 nm, Epot= -1.05838e+04 Fmax= 7.90194e+04, atom= 818\n",
      "Step=   20, Dmax= 1.3e-01 nm, Epot= -1.44387e+04 Fmax= 1.77139e+04, atom= 1591\n",
      "Step=   22, Dmax= 8.0e-02 nm, Epot= -1.69178e+04 Fmax= 2.36072e+04, atom= 1591\n",
      "Step=   23, Dmax= 9.6e-02 nm, Epot= -1.85681e+04 Fmax= 1.69728e+04, atom= 1267\n",
      "Step=   24, Dmax= 1.2e-01 nm, Epot= -2.05149e+04 Fmax= 1.35050e+04, atom= 1586\n",
      "Step=   26, Dmax= 6.9e-02 nm, Epot= -2.22956e+04 Fmax= 7.78836e+03, atom= 1606\n",
      "Step=   27, Dmax= 8.3e-02 nm, Epot= -2.46064e+04 Fmax= 8.23711e+03, atom= 1606\n",
      "Step=   28, Dmax= 9.9e-02 nm, Epot= -2.60463e+04 Fmax= 2.03933e+04, atom= 1586\n",
      "Step=   29, Dmax= 1.2e-01 nm, Epot= -2.71109e+04 Fmax= 8.51193e+03, atom= 1267\n",
      "Step=   30, Dmax= 1.4e-01 nm, Epot= -2.77852e+04 Fmax= 5.10258e+04, atom= 1490\n",
      "Step=   31, Dmax= 1.7e-01 nm, Epot= -2.89093e+04 Fmax= 8.58690e+03, atom= 1446\n",
      "Step=   32, Dmax= 2.1e-01 nm, Epot= -3.02287e+04 Fmax= 2.27404e+04, atom= 1550\n",
      "Step=   34, Dmax= 1.2e-01 nm, Epot= -3.08777e+04 Fmax= 1.66820e+04, atom= 1550\n",
      "Step=   35, Dmax= 1.5e-01 nm, Epot= -3.15210e+04 Fmax= 7.84227e+03, atom= 468\n",
      "Step=   36, Dmax= 1.8e-01 nm, Epot= -3.26742e+04 Fmax= 4.75746e+03, atom= 1596\n",
      "Step=   37, Dmax= 2.1e-01 nm, Epot= -3.33775e+04 Fmax= 3.33251e+04, atom= 1461\n",
      "Step=   38, Dmax= 2.6e-01 nm, Epot= -3.44663e+04 Fmax= 4.50561e+03, atom= 1596\n",
      "Step=   40, Dmax= 1.5e-01 nm, Epot= -3.54502e+04 Fmax= 1.55014e+03, atom= 430\n",
      "Step=   41, Dmax= 1.8e-01 nm, Epot= -3.68978e+04 Fmax= 1.01690e+04, atom= 430\n",
      "Step=   43, Dmax= 1.1e-01 nm, Epot= -3.73994e+04 Fmax= 2.71559e+03, atom= 1090\n",
      "Step=   44, Dmax= 1.3e-01 nm, Epot= -3.78346e+04 Fmax= 2.32965e+03, atom= 1200\n",
      "Step=   45, Dmax= 1.6e-01 nm, Epot= -3.80156e+04 Fmax= 6.23591e+03, atom= 1363\n",
      "Step=   47, Dmax= 9.6e-02 nm, Epot= -3.85621e+04 Fmax= 2.23179e+03, atom= 867\n",
      "Step=   48, Dmax= 1.1e-01 nm, Epot= -3.89186e+04 Fmax= 1.51574e+03, atom= 666\n",
      "Step=   50, Dmax= 6.9e-02 nm, Epot= -3.92438e+04 Fmax= 1.20551e+03, atom= 1190\n",
      "Step=   52, Dmax= 4.1e-02 nm, Epot= -3.94255e+04 Fmax= 1.81594e+03, atom= 1190\n",
      "Step=   53, Dmax= 5.0e-02 nm, Epot= -3.95620e+04 Fmax= 1.81514e+03, atom= 1190\n",
      "Step=   54, Dmax= 6.0e-02 nm, Epot= -3.96129e+04 Fmax= 3.54761e+03, atom= 1190\n",
      "Step=   55, Dmax= 7.1e-02 nm, Epot= -3.97852e+04 Fmax= 1.91578e+03, atom= 652\n",
      "Step=   57, Dmax= 4.3e-02 nm, Epot= -3.99180e+04 Fmax= 1.12184e+03, atom= 1469\n",
      "Step=   58, Dmax= 5.1e-02 nm, Epot= -4.00826e+04 Fmax= 1.67238e+03, atom= 652\n",
      "Step=   59, Dmax= 6.2e-02 nm, Epot= -4.01535e+04 Fmax= 2.68774e+03, atom= 652\n",
      "Step=   60, Dmax= 7.4e-02 nm, Epot= -4.02825e+04 Fmax= 2.17868e+03, atom= 1190\n",
      "Step=   61, Dmax= 8.9e-02 nm, Epot= -4.03033e+04 Fmax= 2.91221e+03, atom= 1190\n",
      "Step=   63, Dmax= 5.3e-02 nm, Epot= -4.05242e+04 Fmax= 7.05796e+02, atom= 5920\n",
      "Step=   64, Dmax= 6.4e-02 nm, Epot= -4.07518e+04 Fmax= 1.27201e+03, atom= 620\n",
      "Step=   66, Dmax= 3.8e-02 nm, Epot= -4.08795e+04 Fmax= 1.06263e+03, atom= 620\n",
      "Step=   67, Dmax= 4.6e-02 nm, Epot= -4.09734e+04 Fmax= 1.25273e+03, atom= 1190\n",
      "Step=   68, Dmax= 5.5e-02 nm, Epot= -4.10696e+04 Fmax= 1.23272e+03, atom= 652\n",
      "Step=   69, Dmax= 6.6e-02 nm, Epot= -4.10939e+04 Fmax= 2.04464e+03, atom= 652\n",
      "Step=   70, Dmax= 8.0e-02 nm, Epot= -4.11802e+04 Fmax= 2.15417e+03, atom= 652\n",
      "Step=   72, Dmax= 4.8e-02 nm, Epot= -4.13412e+04 Fmax= 5.26577e+02, atom= 1469\n",
      "Step=   73, Dmax= 5.7e-02 nm, Epot= -4.14448e+04 Fmax= 4.39032e+03, atom= 113\n",
      "Step=   74, Dmax= 6.9e-02 nm, Epot= -4.15754e+04 Fmax= 1.06623e+03, atom= 170\n",
      "Step=   75, Dmax= 8.3e-02 nm, Epot= -4.16106e+04 Fmax= 4.02645e+03, atom= 170\n",
      "Step=   76, Dmax= 9.9e-02 nm, Epot= -4.17108e+04 Fmax= 1.42297e+03, atom= 113\n",
      "Step=   78, Dmax= 5.9e-02 nm, Epot= -4.18203e+04 Fmax= 6.25564e+02, atom= 1281\n",
      "Step=   79, Dmax= 7.1e-02 nm, Epot= -4.19431e+04 Fmax= 1.31156e+03, atom= 1281\n",
      "Step=   81, Dmax= 4.3e-02 nm, Epot= -4.20475e+04 Fmax= 6.75956e+02, atom= 170\n",
      "Step=   82, Dmax= 5.1e-02 nm, Epot= -4.21342e+04 Fmax= 8.44703e+02, atom= 170\n",
      "Step=   83, Dmax= 6.2e-02 nm, Epot= -4.22080e+04 Fmax= 1.08376e+03, atom= 170\n",
      "Step=   84, Dmax= 7.4e-02 nm, Epot= -4.22579e+04 Fmax= 1.35636e+03, atom= 170\n",
      "Step=   85, Dmax= 8.9e-02 nm, Epot= -4.23002e+04 Fmax= 1.18031e+03, atom= 1281\n",
      "Step=   87, Dmax= 5.3e-02 nm, Epot= -4.24241e+04 Fmax= 5.93261e+02, atom= 240\n",
      "Step=   88, Dmax= 6.4e-02 nm, Epot= -4.24516e+04 Fmax= 1.85303e+03, atom= 850\n",
      "Step=   89, Dmax= 7.7e-02 nm, Epot= -4.25603e+04 Fmax= 1.13979e+03, atom= 850\n",
      "Step=   91, Dmax= 4.6e-02 nm, Epot= -4.26388e+04 Fmax= 4.70422e+02, atom= 70\n",
      "Step=   92, Dmax= 5.5e-02 nm, Epot= -4.27223e+04 Fmax= 7.49647e+02, atom= 70\n",
      "Step=   94, Dmax= 3.3e-02 nm, Epot= -4.27898e+04 Fmax= 3.79446e+02, atom= 1589\n",
      "Step=   95, Dmax= 4.0e-02 nm, Epot= -4.28411e+04 Fmax= 1.38630e+03, atom= 1589\n",
      "Step=   96, Dmax= 4.8e-02 nm, Epot= -4.29084e+04 Fmax= 4.60233e+02, atom= 434\n",
      "Step=   97, Dmax= 5.7e-02 nm, Epot= -4.29653e+04 Fmax= 1.77860e+03, atom= 434\n",
      "Step=   98, Dmax= 6.9e-02 nm, Epot= -4.30177e+04 Fmax= 6.70254e+02, atom= 1589\n",
      "Step=  100, Dmax= 4.1e-02 nm, Epot= -4.30756e+04 Fmax= 4.30153e+02, atom= 3179\n",
      "Step=  101, Dmax= 4.9e-02 nm, Epot= -4.31321e+04 Fmax= 8.24552e+02, atom= 1589\n",
      "Step=  102, Dmax= 5.9e-02 nm, Epot= -4.31471e+04 Fmax= 1.75411e+03, atom= 1589\n",
      "Step=  103, Dmax= 7.1e-02 nm, Epot= -4.32164e+04 Fmax= 6.37465e+02, atom= 434\n",
      "Step=  104, Dmax= 8.5e-02 nm, Epot= -4.32407e+04 Fmax= 2.03419e+03, atom= 434\n",
      "Step=  105, Dmax= 1.0e-01 nm, Epot= -4.32805e+04 Fmax= 1.15510e+03, atom= 1589\n",
      "Step=  107, Dmax= 6.2e-02 nm, Epot= -4.33413e+04 Fmax= 7.60702e+02, atom= 317\n",
      "Step=  108, Dmax= 7.4e-02 nm, Epot= -4.33930e+04 Fmax= 5.24166e+02, atom= 421\n",
      "Step=  110, Dmax= 4.4e-02 nm, Epot= -4.34409e+04 Fmax= 4.94250e+02, atom= 1310\n",
      "Step=  111, Dmax= 5.3e-02 nm, Epot= -4.34520e+04 Fmax= 7.46669e+02, atom= 809\n",
      "Step=  112, Dmax= 6.4e-02 nm, Epot= -4.34530e+04 Fmax= 1.01330e+03, atom= 1338\n",
      "Step=  113, Dmax= 7.7e-02 nm, Epot= -4.34772e+04 Fmax= 9.73190e+02, atom= 1338\n",
      "Step=  115, Dmax= 4.6e-02 nm, Epot= -4.36055e+04 Fmax= 2.26279e+02, atom= 8764\n",
      "Step=  117, Dmax= 2.8e-02 nm, Epot= -4.36482e+04 Fmax= 3.53046e+02, atom= 9764\n",
      "Step=  118, Dmax= 3.3e-02 nm, Epot= -4.36615e+04 Fmax= 5.72281e+02, atom= 97\n",
      "Step=  119, Dmax= 4.0e-02 nm, Epot= -4.37004e+04 Fmax= 5.89451e+02, atom= 97\n",
      "Step=  120, Dmax= 4.8e-02 nm, Epot= -4.37113e+04 Fmax= 7.40817e+02, atom= 97\n",
      "Step=  121, Dmax= 5.7e-02 nm, Epot= -4.37209e+04 Fmax= 8.89442e+02, atom= 97\n",
      "Step=  123, Dmax= 3.4e-02 nm, Epot= -4.37990e+04 Fmax= 2.50053e+02, atom= 292\n",
      "Step=  124, Dmax= 4.1e-02 nm, Epot= -4.38149e+04 Fmax= 1.67266e+03, atom= 983\n",
      "Step=  125, Dmax= 4.9e-02 nm, Epot= -4.38634e+04 Fmax= 4.25221e+02, atom= 983\n",
      "Step=  127, Dmax= 3.0e-02 nm, Epot= -4.38911e+04 Fmax= 2.60399e+02, atom= 983\n",
      "Step=  128, Dmax= 3.6e-02 nm, Epot= -4.39122e+04 Fmax= 8.88130e+02, atom= 983\n",
      "Step=  129, Dmax= 4.3e-02 nm, Epot= -4.39451e+04 Fmax= 4.05544e+02, atom= 983\n",
      "Step=  131, Dmax= 2.6e-02 nm, Epot= -4.39673e+04 Fmax= 2.67327e+02, atom= 983\n",
      "Step=  132, Dmax= 3.1e-02 nm, Epot= -4.39873e+04 Fmax= 7.50607e+02, atom= 983\n",
      "Step=  133, Dmax= 3.7e-02 nm, Epot= -4.40119e+04 Fmax= 3.91773e+02, atom= 983\n",
      "Step=  134, Dmax= 4.4e-02 nm, Epot= -4.40212e+04 Fmax= 1.06100e+03, atom= 983\n",
      "Step=  135, Dmax= 5.3e-02 nm, Epot= -4.40482e+04 Fmax= 5.30381e+02, atom= 983\n",
      "Step=  137, Dmax= 3.2e-02 nm, Epot= -4.40755e+04 Fmax= 2.33595e+02, atom= 1550\n",
      "Step=  138, Dmax= 3.8e-02 nm, Epot= -4.40792e+04 Fmax= 1.02432e+03, atom= 983\n",
      "Step=  139, Dmax= 4.6e-02 nm, Epot= -4.41246e+04 Fmax= 5.36538e+02, atom= 983\n",
      "Step=  140, Dmax= 5.5e-02 nm, Epot= -4.41284e+04 Fmax= 8.92441e+02, atom= 983\n",
      "Step=  141, Dmax= 6.6e-02 nm, Epot= -4.41372e+04 Fmax= 9.81172e+02, atom= 983\n",
      "Step=  143, Dmax= 4.0e-02 nm, Epot= -4.41830e+04 Fmax= 2.21421e+02, atom= 292\n",
      "Step=  144, Dmax= 4.8e-02 nm, Epot= -4.41959e+04 Fmax= 9.82634e+02, atom= 681\n",
      "Step=  145, Dmax= 5.7e-02 nm, Epot= -4.42008e+04 Fmax= 1.27957e+03, atom= 983\n",
      "Step=  146, Dmax= 6.8e-02 nm, Epot= -4.42377e+04 Fmax= 5.80174e+02, atom= 983\n",
      "Step=  148, Dmax= 4.1e-02 nm, Epot= -4.42668e+04 Fmax= 3.80146e+02, atom= 681\n",
      "Step=  150, Dmax= 2.5e-02 nm, Epot= -4.42906e+04 Fmax= 1.43903e+02, atom= 681\n",
      "Step=  151, Dmax= 3.0e-02 nm, Epot= -4.42986e+04 Fmax= 8.00341e+02, atom= 681\n",
      "Step=  152, Dmax= 3.5e-02 nm, Epot= -4.43427e+04 Fmax= 2.10513e+02, atom= 681\n",
      "Step=  154, Dmax= 2.1e-02 nm, Epot= -4.43587e+04 Fmax= 3.21124e+02, atom= 681\n",
      "Step=  155, Dmax= 2.6e-02 nm, Epot= -4.43728e+04 Fmax= 3.68379e+02, atom= 681\n",
      "Step=  156, Dmax= 3.1e-02 nm, Epot= -4.43838e+04 Fmax= 4.31187e+02, atom= 681\n",
      "Step=  157, Dmax= 3.7e-02 nm, Epot= -4.43941e+04 Fmax= 5.81376e+02, atom= 681\n",
      "Step=  158, Dmax= 4.4e-02 nm, Epot= -4.44034e+04 Fmax= 5.63750e+02, atom= 681\n",
      "Step=  160, Dmax= 2.6e-02 nm, Epot= -4.44308e+04 Fmax= 9.28600e+01, atom= 983\n",
      "Step=  161, Dmax= 3.2e-02 nm, Epot= -4.44547e+04 Fmax= 8.00824e+02, atom= 983\n",
      "Step=  162, Dmax= 3.8e-02 nm, Epot= -4.44837e+04 Fmax= 4.80872e+02, atom= 681\n",
      "Step=  164, Dmax= 2.3e-02 nm, Epot= -4.44992e+04 Fmax= 2.08877e+02, atom= 681\n",
      "Step=  165, Dmax= 2.7e-02 nm, Epot= -4.45087e+04 Fmax= 5.78343e+02, atom= 681\n",
      "Step=  166, Dmax= 3.3e-02 nm, Epot= -4.45223e+04 Fmax= 3.13594e+02, atom= 681\n",
      "Step=  168, Dmax= 2.0e-02 nm, Epot= -4.45345e+04 Fmax= 1.32850e+02, atom= 681\n",
      "Step=  169, Dmax= 2.4e-02 nm, Epot= -4.45434e+04 Fmax= 5.16686e+02, atom= 681\n",
      "Step=  170, Dmax= 2.8e-02 nm, Epot= -4.45622e+04 Fmax= 2.22004e+02, atom= 681\n",
      "Step=  172, Dmax= 1.7e-02 nm, Epot= -4.45718e+04 Fmax= 2.13735e+02, atom= 681\n",
      "Step=  173, Dmax= 2.1e-02 nm, Epot= -4.45806e+04 Fmax= 3.12405e+02, atom= 681\n",
      "Step=  174, Dmax= 2.5e-02 nm, Epot= -4.45886e+04 Fmax= 3.18511e+02, atom= 681\n",
      "Step=  175, Dmax= 3.0e-02 nm, Epot= -4.45949e+04 Fmax= 4.49565e+02, atom= 681\n",
      "Step=  176, Dmax= 3.5e-02 nm, Epot= -4.46012e+04 Fmax= 4.41628e+02, atom= 681\n",
      "Step=  177, Dmax= 4.3e-02 nm, Epot= -4.46024e+04 Fmax= 6.80731e+02, atom= 681\n",
      "Step=  178, Dmax= 5.1e-02 nm, Epot= -4.46087e+04 Fmax= 5.79259e+02, atom= 681\n",
      "Step=  180, Dmax= 3.1e-02 nm, Epot= -4.46340e+04 Fmax= 1.09441e+02, atom= 983\n",
      "Step=  182, Dmax= 1.8e-02 nm, Epot= -4.46458e+04 Fmax= 2.53528e+02, atom= 983\n",
      "Step=  183, Dmax= 2.2e-02 nm, Epot= -4.46526e+04 Fmax= 3.37533e+02, atom= 681\n",
      "Step=  184, Dmax= 2.6e-02 nm, Epot= -4.46607e+04 Fmax= 3.22827e+02, atom= 681\n",
      "Step=  185, Dmax= 3.2e-02 nm, Epot= -4.46640e+04 Fmax= 4.85920e+02, atom= 681\n",
      "Step=  186, Dmax= 3.8e-02 nm, Epot= -4.46706e+04 Fmax= 4.41631e+02, atom= 681\n",
      "Step=  188, Dmax= 2.3e-02 nm, Epot= -4.46878e+04 Fmax= 6.99539e+01, atom= 983\n",
      "Step=  189, Dmax= 2.7e-02 nm, Epot= -4.46916e+04 Fmax= 6.72942e+02, atom= 983\n",
      "Step=  190, Dmax= 3.3e-02 nm, Epot= -4.47196e+04 Fmax= 3.42267e+02, atom= 681\n",
      "Step=  192, Dmax= 2.0e-02 nm, Epot= -4.47291e+04 Fmax= 1.69135e+02, atom= 681\n",
      "Step=  193, Dmax= 2.4e-02 nm, Epot= -4.47341e+04 Fmax= 4.38089e+02, atom= 681\n",
      "Step=  194, Dmax= 2.8e-02 nm, Epot= -4.47428e+04 Fmax= 2.60042e+02, atom= 681\n",
      "Step=  196, Dmax= 1.7e-02 nm, Epot= -4.47509e+04 Fmax= 1.00247e+02, atom= 681\n",
      "Step=  197, Dmax= 2.0e-02 nm, Epot= -4.47564e+04 Fmax= 4.08079e+02, atom= 681\n",
      "Step=  198, Dmax= 2.5e-02 nm, Epot= -4.47696e+04 Fmax= 1.69258e+02, atom= 681\n",
      "Step=  200, Dmax= 1.5e-02 nm, Epot= -4.47760e+04 Fmax= 1.79183e+02, atom= 681\n",
      "Step=  201, Dmax= 1.8e-02 nm, Epot= -4.47820e+04 Fmax= 2.30397e+02, atom= 681\n",
      "Step=  202, Dmax= 2.1e-02 nm, Epot= -4.47871e+04 Fmax= 2.66957e+02, atom= 681\n",
      "Step=  203, Dmax= 2.5e-02 nm, Epot= -4.47922e+04 Fmax= 3.29333e+02, atom= 681\n",
      "Step=  204, Dmax= 3.1e-02 nm, Epot= -4.47953e+04 Fmax= 3.71861e+02, atom= 681\n",
      "Step=  205, Dmax= 3.7e-02 nm, Epot= -4.47976e+04 Fmax= 4.93454e+02, atom= 681\n",
      "Step=  206, Dmax= 4.4e-02 nm, Epot= -4.47986e+04 Fmax= 4.95148e+02, atom= 681\n",
      "Step=  208, Dmax= 2.6e-02 nm, Epot= -4.48210e+04 Fmax= 6.43185e+01, atom= 983\n",
      "Step=  210, Dmax= 1.6e-02 nm, Epot= -4.48271e+04 Fmax= 2.21498e+02, atom= 681\n",
      "Step=  211, Dmax= 1.9e-02 nm, Epot= -4.48332e+04 Fmax= 2.63512e+02, atom= 642\n",
      "Step=  212, Dmax= 2.3e-02 nm, Epot= -4.48369e+04 Fmax= 2.88733e+02, atom= 642\n",
      "Step=  213, Dmax= 2.7e-02 nm, Epot= -4.48374e+04 Fmax= 4.27319e+02, atom= 642\n",
      "Step=  214, Dmax= 3.3e-02 nm, Epot= -4.48457e+04 Fmax= 3.65651e+02, atom= 642\n",
      "Step=  216, Dmax= 2.0e-02 nm, Epot= -4.48645e+04 Fmax= 6.75728e+01, atom= 566\n",
      "Step=  218, Dmax= 1.2e-02 nm, Epot= -4.48702e+04 Fmax= 2.10278e+02, atom= 642\n",
      "Step=  219, Dmax= 1.4e-02 nm, Epot= -4.48787e+04 Fmax= 1.59517e+02, atom= 642\n",
      "Step=  220, Dmax= 1.7e-02 nm, Epot= -4.48816e+04 Fmax= 2.37098e+02, atom= 642\n",
      "Step=  221, Dmax= 2.0e-02 nm, Epot= -4.48863e+04 Fmax= 2.64822e+02, atom= 642\n",
      "Step=  222, Dmax= 2.5e-02 nm, Epot= -4.48878e+04 Fmax= 3.15225e+02, atom= 642\n",
      "Step=  223, Dmax= 2.9e-02 nm, Epot= -4.48880e+04 Fmax= 4.17213e+02, atom= 642\n",
      "Step=  224, Dmax= 3.5e-02 nm, Epot= -4.48898e+04 Fmax= 4.16968e+02, atom= 642\n",
      "Step=  226, Dmax= 2.1e-02 nm, Epot= -4.49124e+04 Fmax= 8.02827e+01, atom= 1517\n",
      "Step=  228, Dmax= 1.3e-02 nm, Epot= -4.49177e+04 Fmax= 2.24192e+02, atom= 809\n",
      "Step=  229, Dmax= 1.5e-02 nm, Epot= -4.49250e+04 Fmax= 1.52218e+02, atom= 809\n",
      "Step=  230, Dmax= 1.8e-02 nm, Epot= -4.49260e+04 Fmax= 2.90450e+02, atom= 809\n",
      "Step=  231, Dmax= 2.2e-02 nm, Epot= -4.49326e+04 Fmax= 2.40121e+02, atom= 809\n",
      "Step=  233, Dmax= 1.3e-02 nm, Epot= -4.49417e+04 Fmax= 6.49885e+01, atom= 401\n",
      "Step=  235, Dmax= 7.9e-03 nm, Epot= -4.49471e+04 Fmax= 1.35759e+02, atom= 401\n",
      "Step=  236, Dmax= 9.5e-03 nm, Epot= -4.49523e+04 Fmax= 1.08182e+02, atom= 401\n",
      "Step=  237, Dmax= 1.1e-02 nm, Epot= -4.49565e+04 Fmax= 1.81130e+02, atom= 401\n",
      "Step=  238, Dmax= 1.4e-02 nm, Epot= -4.49614e+04 Fmax= 1.69196e+02, atom= 401\n",
      "Step=  239, Dmax= 1.6e-02 nm, Epot= -4.49645e+04 Fmax= 2.52875e+02, atom= 401\n",
      "Step=  240, Dmax= 2.0e-02 nm, Epot= -4.49692e+04 Fmax= 2.50626e+02, atom= 401\n",
      "Step=  241, Dmax= 2.4e-02 nm, Epot= -4.49705e+04 Fmax= 3.65892e+02, atom= 401\n",
      "Step=  242, Dmax= 2.8e-02 nm, Epot= -4.49751e+04 Fmax= 3.59765e+02, atom= 401\n",
      "Step=  244, Dmax= 1.7e-02 nm, Epot= -4.49854e+04 Fmax= 6.73207e+01, atom= 401\n",
      "Step=  246, Dmax= 1.0e-02 nm, Epot= -4.49913e+04 Fmax= 2.18625e+02, atom= 401\n",
      "Step=  247, Dmax= 1.2e-02 nm, Epot= -4.49966e+04 Fmax= 1.06170e+02, atom= 401\n",
      "Step=  248, Dmax= 1.5e-02 nm, Epot= -4.50010e+04 Fmax= 2.67906e+02, atom= 401\n",
      "Step=  249, Dmax= 1.8e-02 nm, Epot= -4.50063e+04 Fmax= 1.80823e+02, atom= 401\n",
      "Step=  250, Dmax= 2.1e-02 nm, Epot= -4.50073e+04 Fmax= 3.71151e+02, atom= 401\n",
      "Step=  251, Dmax= 2.5e-02 nm, Epot= -4.50133e+04 Fmax= 2.91756e+02, atom= 401\n",
      "Step=  253, Dmax= 1.5e-02 nm, Epot= -4.50202e+04 Fmax= 9.03754e+01, atom= 401\n",
      "Step=  254, Dmax= 1.8e-02 nm, Epot= -4.50237e+04 Fmax= 4.05349e+02, atom= 401\n",
      "Step=  255, Dmax= 2.2e-02 nm, Epot= -4.50323e+04 Fmax= 1.73953e+02, atom= 401\n",
      "Step=  257, Dmax= 1.3e-02 nm, Epot= -4.50365e+04 Fmax= 1.37803e+02, atom= 401\n",
      "Step=  258, Dmax= 1.6e-02 nm, Epot= -4.50395e+04 Fmax= 2.67295e+02, atom= 401\n",
      "Step=  259, Dmax= 1.9e-02 nm, Epot= -4.50443e+04 Fmax= 2.16125e+02, atom= 401\n",
      "Step=  260, Dmax= 2.3e-02 nm, Epot= -4.50449e+04 Fmax= 3.64110e+02, atom= 401\n",
      "Step=  261, Dmax= 2.7e-02 nm, Epot= -4.50491e+04 Fmax= 3.46302e+02, atom= 401\n",
      "Step=  263, Dmax= 1.6e-02 nm, Epot= -4.50579e+04 Fmax= 6.90870e+01, atom= 401\n",
      "Step=  264, Dmax= 2.0e-02 nm, Epot= -4.50631e+04 Fmax= 4.63914e+02, atom= 401\n",
      "Step=  265, Dmax= 2.4e-02 nm, Epot= -4.50730e+04 Fmax= 1.72436e+02, atom= 401\n",
      "Step=  267, Dmax= 1.4e-02 nm, Epot= -4.50768e+04 Fmax= 1.59719e+02, atom= 401\n",
      "Step=  268, Dmax= 1.7e-02 nm, Epot= -4.50793e+04 Fmax= 2.67016e+02, atom= 401\n",
      "Step=  269, Dmax= 2.0e-02 nm, Epot= -4.50833e+04 Fmax= 2.47747e+02, atom= 401\n",
      "Step=  270, Dmax= 2.4e-02 nm, Epot= -4.50836e+04 Fmax= 3.68733e+02, atom= 401\n",
      "Step=  271, Dmax= 2.9e-02 nm, Epot= -4.50861e+04 Fmax= 3.95854e+02, atom= 401\n",
      "Step=  273, Dmax= 1.8e-02 nm, Epot= -4.50968e+04 Fmax= 5.60686e+01, atom= 401\n",
      "Step=  274, Dmax= 2.1e-02 nm, Epot= -4.51039e+04 Fmax= 5.17311e+02, atom= 401\n",
      "Step=  275, Dmax= 2.5e-02 nm, Epot= -4.51143e+04 Fmax= 1.85720e+02, atom= 401\n",
      "Step=  277, Dmax= 1.5e-02 nm, Epot= -4.51178e+04 Fmax= 1.75657e+02, atom= 401\n",
      "Step=  278, Dmax= 1.8e-02 nm, Epot= -4.51196e+04 Fmax= 2.78257e+02, atom= 401\n",
      "Step=  279, Dmax= 2.2e-02 nm, Epot= -4.51230e+04 Fmax= 2.73040e+02, atom= 401\n",
      "Step=  281, Dmax= 1.3e-02 nm, Epot= -4.51292e+04 Fmax= 5.69754e+01, atom= 401\n",
      "Step=  282, Dmax= 1.6e-02 nm, Epot= -4.51354e+04 Fmax= 3.42278e+02, atom= 401\n",
      "Step=  283, Dmax= 1.9e-02 nm, Epot= -4.51422e+04 Fmax= 1.44151e+02, atom= 401\n",
      "Step=  285, Dmax= 1.1e-02 nm, Epot= -4.51455e+04 Fmax= 1.24741e+02, atom= 401\n",
      "Step=  286, Dmax= 1.4e-02 nm, Epot= -4.51481e+04 Fmax= 2.14771e+02, atom= 401\n",
      "Step=  287, Dmax= 1.6e-02 nm, Epot= -4.51516e+04 Fmax= 1.94119e+02, atom= 401\n",
      "Step=  288, Dmax= 2.0e-02 nm, Epot= -4.51526e+04 Fmax= 2.94393e+02, atom= 401\n",
      "Step=  289, Dmax= 2.4e-02 nm, Epot= -4.51553e+04 Fmax= 3.07843e+02, atom= 401\n",
      "Step=  291, Dmax= 1.4e-02 nm, Epot= -4.51628e+04 Fmax= 5.11250e+01, atom= 401\n",
      "Step=  292, Dmax= 1.7e-02 nm, Epot= -4.51698e+04 Fmax= 3.67684e+02, atom= 401\n",
      "Step=  293, Dmax= 2.0e-02 nm, Epot= -4.51767e+04 Fmax= 1.53383e+02, atom= 401\n",
      "Step=  295, Dmax= 1.2e-02 nm, Epot= -4.51798e+04 Fmax= 1.39341e+02, atom= 401\n",
      "Step=  296, Dmax= 1.5e-02 nm, Epot= -4.51818e+04 Fmax= 2.21630e+02, atom= 401\n",
      "Step=  297, Dmax= 1.8e-02 nm, Epot= -4.51849e+04 Fmax= 2.19558e+02, atom= 401\n",
      "Step=  298, Dmax= 2.1e-02 nm, Epot= -4.51857e+04 Fmax= 3.01374e+02, atom= 401\n",
      "Step=  299, Dmax= 2.5e-02 nm, Epot= -4.51871e+04 Fmax= 3.50012e+02, atom= 401\n",
      "Step=  300, Dmax= 3.0e-02 nm, Epot= -4.51874e+04 Fmax= 4.01144e+02, atom= 401\n",
      "Step=  302, Dmax= 1.8e-02 nm, Epot= -4.51991e+04 Fmax= 7.91110e+01, atom= 732\n",
      "Step=  303, Dmax= 2.2e-02 nm, Epot= -4.51996e+04 Fmax= 4.03636e+02, atom= 732\n",
      "Step=  304, Dmax= 2.6e-02 nm, Epot= -4.52062e+04 Fmax= 3.25164e+02, atom= 401\n",
      "Step=  306, Dmax= 1.6e-02 nm, Epot= -4.52135e+04 Fmax= 8.16744e+01, atom= 401\n",
      "Step=  307, Dmax= 1.9e-02 nm, Epot= -4.52162e+04 Fmax= 3.57140e+02, atom= 401\n",
      "Step=  308, Dmax= 2.3e-02 nm, Epot= -4.52222e+04 Fmax= 1.83389e+02, atom= 401\n",
      "Step=  310, Dmax= 1.4e-02 nm, Epot= -4.52256e+04 Fmax= 1.33658e+02, atom= 401\n",
      "Step=  311, Dmax= 1.6e-02 nm, Epot= -4.52262e+04 Fmax= 2.66531e+02, atom= 401\n",
      "Step=  312, Dmax= 2.0e-02 nm, Epot= -4.52303e+04 Fmax= 2.27669e+02, atom= 401\n",
      "Step=  314, Dmax= 1.2e-02 nm, Epot= -4.52355e+04 Fmax= 6.32919e+01, atom= 401\n",
      "Step=  315, Dmax= 1.4e-02 nm, Epot= -4.52396e+04 Fmax= 2.64077e+02, atom= 401\n",
      "Step=  316, Dmax= 1.7e-02 nm, Epot= -4.52444e+04 Fmax= 1.42809e+02, atom= 401\n",
      "Step=  318, Dmax= 1.0e-02 nm, Epot= -4.52476e+04 Fmax= 9.54287e+01, atom= 401\n",
      "Step=  319, Dmax= 1.2e-02 nm, Epot= -4.52497e+04 Fmax= 2.01162e+02, atom= 401\n",
      "Step=  320, Dmax= 1.5e-02 nm, Epot= -4.52533e+04 Fmax= 1.60504e+02, atom= 401\n",
      "Step=  321, Dmax= 1.8e-02 nm, Epot= -4.52539e+04 Fmax= 2.62924e+02, atom= 401\n",
      "Step=  322, Dmax= 2.1e-02 nm, Epot= -4.52566e+04 Fmax= 2.67672e+02, atom= 401\n",
      "Step=  324, Dmax= 1.3e-02 nm, Epot= -4.52632e+04 Fmax= 4.78890e+01, atom= 401\n",
      "Step=  325, Dmax= 1.5e-02 nm, Epot= -4.52696e+04 Fmax= 2.89863e+02, atom= 401\n",
      "Step=  326, Dmax= 1.8e-02 nm, Epot= -4.52745e+04 Fmax= 1.46259e+02, atom= 1356\n",
      "Step=  328, Dmax= 1.1e-02 nm, Epot= -4.52774e+04 Fmax= 1.08762e+02, atom= 401\n",
      "Step=  329, Dmax= 1.3e-02 nm, Epot= -4.52790e+04 Fmax= 2.08804e+02, atom= 1356\n",
      "Step=  330, Dmax= 1.6e-02 nm, Epot= -4.52823e+04 Fmax= 1.72575e+02, atom= 401\n",
      "Step=  332, Dmax= 9.4e-03 nm, Epot= -4.52861e+04 Fmax= 5.70415e+01, atom= 4016\n",
      "Step=  333, Dmax= 1.1e-02 nm, Epot= -4.52898e+04 Fmax= 2.05683e+02, atom= 401\n",
      "Step=  334, Dmax= 1.4e-02 nm, Epot= -4.52935e+04 Fmax= 1.13823e+02, atom= 401\n",
      "Step=  336, Dmax= 8.1e-03 nm, Epot= -4.52962e+04 Fmax= 7.54581e+01, atom= 401\n",
      "Step=  337, Dmax= 9.8e-03 nm, Epot= -4.52985e+04 Fmax= 1.61216e+02, atom= 1356\n",
      "Step=  338, Dmax= 1.2e-02 nm, Epot= -4.53015e+04 Fmax= 1.20143e+02, atom= 1356\n",
      "Step=  339, Dmax= 1.4e-02 nm, Epot= -4.53025e+04 Fmax= 2.19162e+02, atom= 1356\n",
      "Step=  340, Dmax= 1.7e-02 nm, Epot= -4.53055e+04 Fmax= 1.87068e+02, atom= 1356\n",
      "Step=  342, Dmax= 1.0e-02 nm, Epot= -4.53095e+04 Fmax= 5.70910e+01, atom= 4016\n",
      "Step=  343, Dmax= 1.2e-02 nm, Epot= -4.53125e+04 Fmax= 2.22705e+02, atom= 401\n",
      "Step=  344, Dmax= 1.5e-02 nm, Epot= -4.53164e+04 Fmax= 1.20191e+02, atom= 1356\n",
      "Step=  346, Dmax= 8.8e-03 nm, Epot= -4.53189e+04 Fmax= 8.00550e+01, atom= 1356\n",
      "Step=  347, Dmax= 1.1e-02 nm, Epot= -4.53206e+04 Fmax= 1.73454e+02, atom= 1356\n",
      "Step=  348, Dmax= 1.3e-02 nm, Epot= -4.53235e+04 Fmax= 1.24943e+02, atom= 1356\n",
      "Step=  349, Dmax= 1.5e-02 nm, Epot= -4.53237e+04 Fmax= 2.38134e+02, atom= 1356\n",
      "Step=  350, Dmax= 1.8e-02 nm, Epot= -4.53269e+04 Fmax= 1.92623e+02, atom= 1356\n",
      "Step=  352, Dmax= 1.1e-02 nm, Epot= -4.53309e+04 Fmax= 6.47061e+01, atom= 4016\n",
      "Step=  353, Dmax= 1.3e-02 nm, Epot= -4.53325e+04 Fmax= 2.33340e+02, atom= 401\n",
      "Step=  354, Dmax= 1.6e-02 nm, Epot= -4.53366e+04 Fmax= 1.32755e+02, atom= 1356\n",
      "Step=  356, Dmax= 9.4e-03 nm, Epot= -4.53391e+04 Fmax= 7.97862e+01, atom= 732\n",
      "Step=  357, Dmax= 1.1e-02 nm, Epot= -4.53402e+04 Fmax= 1.90449e+02, atom= 1356\n",
      "Step=  358, Dmax= 1.4e-02 nm, Epot= -4.53434e+04 Fmax= 1.26101e+02, atom= 1356\n",
      "Step=  360, Dmax= 8.1e-03 nm, Epot= -4.53459e+04 Fmax= 5.88508e+01, atom= 4016\n",
      "Step=  361, Dmax= 9.8e-03 nm, Epot= -4.53478e+04 Fmax= 1.65977e+02, atom= 401\n",
      "Step=  362, Dmax= 1.2e-02 nm, Epot= -4.53508e+04 Fmax= 1.05645e+02, atom= 1356\n",
      "Step=  363, Dmax= 1.4e-02 nm, Epot= -4.53508e+04 Fmax= 2.19347e+02, atom= 1356\n",
      "Step=  364, Dmax= 1.7e-02 nm, Epot= -4.53540e+04 Fmax= 1.71196e+02, atom= 1356\n",
      "Step=  366, Dmax= 1.0e-02 nm, Epot= -4.53574e+04 Fmax= 6.38905e+01, atom= 7326\n",
      "Step=  367, Dmax= 1.2e-02 nm, Epot= -4.53585e+04 Fmax= 2.11677e+02, atom= 732\n",
      "Step=  368, Dmax= 1.5e-02 nm, Epot= -4.53621e+04 Fmax= 1.23472e+02, atom= 1356\n",
      "Step=  370, Dmax= 8.7e-03 nm, Epot= -4.53644e+04 Fmax= 6.90884e+01, atom= 1356\n",
      "Step=  371, Dmax= 1.0e-02 nm, Epot= -4.53655e+04 Fmax= 1.70116e+02, atom= 1356\n",
      "Step=  372, Dmax= 1.3e-02 nm, Epot= -4.53684e+04 Fmax= 1.17780e+02, atom= 1356\n",
      "Step=  374, Dmax= 7.6e-03 nm, Epot= -4.53708e+04 Fmax= 5.43108e+01, atom= 7326\n",
      "Step=  375, Dmax= 9.1e-03 nm, Epot= -4.53727e+04 Fmax= 1.49716e+02, atom= 732\n",
      "Step=  376, Dmax= 1.1e-02 nm, Epot= -4.53752e+04 Fmax= 9.37573e+01, atom= 732\n",
      "Step=  377, Dmax= 1.3e-02 nm, Epot= -4.53753e+04 Fmax= 2.13574e+02, atom= 732\n",
      "Step=  378, Dmax= 1.6e-02 nm, Epot= -4.53787e+04 Fmax= 1.38101e+02, atom= 732\n",
      "Step=  380, Dmax= 9.4e-03 nm, Epot= -4.53813e+04 Fmax= 6.41603e+01, atom= 1356\n",
      "Step=  381, Dmax= 1.1e-02 nm, Epot= -4.53816e+04 Fmax= 1.92141e+02, atom= 1356\n",
      "Step=  382, Dmax= 1.4e-02 nm, Epot= -4.53854e+04 Fmax= 1.15458e+02, atom= 732\n",
      "Step=  384, Dmax= 8.1e-03 nm, Epot= -4.53877e+04 Fmax= 6.75705e+01, atom= 7326\n",
      "Step=  385, Dmax= 9.7e-03 nm, Epot= -4.53890e+04 Fmax= 1.47951e+02, atom= 732\n",
      "Step=  386, Dmax= 1.2e-02 nm, Epot= -4.53914e+04 Fmax= 1.09483e+02, atom= 732\n",
      "Step=  388, Dmax= 7.0e-03 nm, Epot= -4.53936e+04 Fmax= 4.14989e+01, atom= 732\n",
      "Step=  389, Dmax= 8.4e-03 nm, Epot= -4.53953e+04 Fmax= 1.47392e+02, atom= 732\n",
      "Step=  390, Dmax= 1.0e-02 nm, Epot= -4.53985e+04 Fmax= 7.96769e+01, atom= 732\n",
      "Step=  392, Dmax= 6.1e-03 nm, Epot= -4.54004e+04 Fmax= 5.41914e+01, atom= 732\n",
      "Step=  393, Dmax= 7.3e-03 nm, Epot= -4.54020e+04 Fmax= 1.05904e+02, atom= 732\n",
      "Step=  394, Dmax= 8.7e-03 nm, Epot= -4.54040e+04 Fmax= 8.51007e+01, atom= 732\n",
      "Step=  395, Dmax= 1.0e-02 nm, Epot= -4.54046e+04 Fmax= 1.49032e+02, atom= 732\n",
      "Step=  396, Dmax= 1.3e-02 nm, Epot= -4.54068e+04 Fmax= 1.31882e+02, atom= 1264\n",
      "Step=  398, Dmax= 7.5e-03 nm, Epot= -4.54100e+04 Fmax= 3.98925e+01, atom= 7184\n",
      "Step=  399, Dmax= 9.0e-03 nm, Epot= -4.54121e+04 Fmax= 1.50702e+02, atom= 718\n",
      "Step=  400, Dmax= 1.1e-02 nm, Epot= -4.54150e+04 Fmax= 9.65127e+01, atom= 1264\n",
      "Step=  402, Dmax= 6.5e-03 nm, Epot= -4.54170e+04 Fmax= 4.84820e+01, atom= 1264\n",
      "Step=  403, Dmax= 7.8e-03 nm, Epot= -4.54188e+04 Fmax= 1.34380e+02, atom= 1264\n",
      "Step=  404, Dmax= 9.4e-03 nm, Epot= -4.54212e+04 Fmax= 7.88978e+01, atom= 1264\n",
      "Step=  405, Dmax= 1.1e-02 nm, Epot= -4.54219e+04 Fmax= 1.84098e+02, atom= 1264\n",
      "Step=  406, Dmax= 1.4e-02 nm, Epot= -4.54247e+04 Fmax= 1.21435e+02, atom= 1264\n",
      "Step=  408, Dmax= 8.1e-03 nm, Epot= -4.54270e+04 Fmax= 5.42474e+01, atom= 1264\n",
      "Step=  409, Dmax= 9.7e-03 nm, Epot= -4.54283e+04 Fmax= 1.67290e+02, atom= 1264\n",
      "Step=  410, Dmax= 1.2e-02 nm, Epot= -4.54313e+04 Fmax= 9.76441e+01, atom= 1264\n",
      "Step=  412, Dmax= 7.0e-03 nm, Epot= -4.54332e+04 Fmax= 5.88133e+01, atom= 1264\n",
      "Step=  413, Dmax= 8.4e-03 nm, Epot= -4.54349e+04 Fmax= 1.36199e+02, atom= 1264\n",
      "Step=  414, Dmax= 1.0e-02 nm, Epot= -4.54371e+04 Fmax= 9.17353e+01, atom= 1264\n",
      "Step=  415, Dmax= 1.2e-02 nm, Epot= -4.54378e+04 Fmax= 1.90666e+02, atom= 1264\n",
      "Step=  416, Dmax= 1.5e-02 nm, Epot= -4.54403e+04 Fmax= 1.37506e+02, atom= 1264\n",
      "Step=  418, Dmax= 8.7e-03 nm, Epot= -4.54429e+04 Fmax= 5.01721e+01, atom= 1264\n",
      "Step=  419, Dmax= 1.0e-02 nm, Epot= -4.54440e+04 Fmax= 1.92386e+02, atom= 1264\n",
      "Step=  420, Dmax= 1.3e-02 nm, Epot= -4.54478e+04 Fmax= 9.50806e+01, atom= 1264\n",
      "Step=  422, Dmax= 7.5e-03 nm, Epot= -4.54497e+04 Fmax= 7.13852e+01, atom= 1264\n",
      "Step=  423, Dmax= 9.0e-03 nm, Epot= -4.54511e+04 Fmax= 1.38056e+02, atom= 1264\n",
      "Step=  424, Dmax= 1.1e-02 nm, Epot= -4.54533e+04 Fmax= 1.06649e+02, atom= 1264\n",
      "Step=  425, Dmax= 1.3e-02 nm, Epot= -4.54538e+04 Fmax= 1.96301e+02, atom= 1264\n",
      "Step=  426, Dmax= 1.6e-02 nm, Epot= -4.54563e+04 Fmax= 1.57068e+02, atom= 1264\n",
      "Step=  428, Dmax= 9.4e-03 nm, Epot= -4.54594e+04 Fmax= 4.62974e+01, atom= 7184\n",
      "Step=  429, Dmax= 1.1e-02 nm, Epot= -4.54602e+04 Fmax= 2.15458e+02, atom= 1264\n",
      "Step=  430, Dmax= 1.3e-02 nm, Epot= -4.54652e+04 Fmax= 9.90192e+01, atom= 1264\n",
      "Step=  432, Dmax= 8.1e-03 nm, Epot= -4.54671e+04 Fmax= 7.86969e+01, atom= 1264\n",
      "Step=  433, Dmax= 9.7e-03 nm, Epot= -4.54684e+04 Fmax= 1.47572e+02, atom= 1264\n",
      "Step=  434, Dmax= 1.2e-02 nm, Epot= -4.54709e+04 Fmax= 1.16005e+02, atom= 1264\n",
      "Step=  435, Dmax= 1.4e-02 nm, Epot= -4.54709e+04 Fmax= 2.11263e+02, atom= 1264\n",
      "Step=  436, Dmax= 1.7e-02 nm, Epot= -4.54738e+04 Fmax= 1.70085e+02, atom= 1264\n",
      "Step=  438, Dmax= 1.0e-02 nm, Epot= -4.54776e+04 Fmax= 5.06155e+01, atom= 7184\n",
      "Step=  439, Dmax= 1.2e-02 nm, Epot= -4.54778e+04 Fmax= 2.24940e+02, atom= 1264\n",
      "Step=  440, Dmax= 1.4e-02 nm, Epot= -4.54834e+04 Fmax= 1.15936e+02, atom= 1264\n",
      "Step=  442, Dmax= 8.7e-03 nm, Epot= -4.54858e+04 Fmax= 7.58463e+01, atom= 1264\n",
      "Step=  443, Dmax= 1.0e-02 nm, Epot= -4.54868e+04 Fmax= 1.71706e+02, atom= 1264\n",
      "Step=  444, Dmax= 1.3e-02 nm, Epot= -4.54899e+04 Fmax= 1.14794e+02, atom= 1264\n",
      "Step=  446, Dmax= 7.5e-03 nm, Epot= -4.54925e+04 Fmax= 5.08589e+01, atom= 1264\n",
      "Step=  447, Dmax= 9.0e-03 nm, Epot= -4.54943e+04 Fmax= 1.55627e+02, atom= 1264\n",
      "Step=  448, Dmax= 1.1e-02 nm, Epot= -4.54977e+04 Fmax= 9.23687e+01, atom= 1264\n",
      "Step=  449, Dmax= 1.3e-02 nm, Epot= -4.54977e+04 Fmax= 2.01794e+02, atom= 1264\n",
      "Step=  450, Dmax= 1.6e-02 nm, Epot= -4.55013e+04 Fmax= 1.54131e+02, atom= 1264\n",
      "Step=  452, Dmax= 9.4e-03 nm, Epot= -4.55048e+04 Fmax= 6.08370e+01, atom= 5824\n",
      "Step=  453, Dmax= 1.1e-02 nm, Epot= -4.55061e+04 Fmax= 2.05291e+02, atom= 1264\n",
      "Step=  454, Dmax= 1.3e-02 nm, Epot= -4.55102e+04 Fmax= 1.10097e+02, atom= 1264\n",
      "Step=  456, Dmax= 8.1e-03 nm, Epot= -4.55126e+04 Fmax= 6.75424e+01, atom= 1264\n",
      "Step=  457, Dmax= 9.7e-03 nm, Epot= -4.55144e+04 Fmax= 1.53591e+02, atom= 1264\n",
      "Step=  458, Dmax= 1.2e-02 nm, Epot= -4.55173e+04 Fmax= 1.13209e+02, atom= 1264\n",
      "Step=  459, Dmax= 1.4e-02 nm, Epot= -4.55178e+04 Fmax= 2.05422e+02, atom= 1264\n",
      "Step=  460, Dmax= 1.7e-02 nm, Epot= -4.55208e+04 Fmax= 1.79725e+02, atom= 1264\n",
      "Step=  462, Dmax= 1.0e-02 nm, Epot= -4.55248e+04 Fmax= 5.70532e+01, atom= 5824\n",
      "Step=  463, Dmax= 1.2e-02 nm, Epot= -4.55270e+04 Fmax= 2.20245e+02, atom= 1264\n",
      "Step=  464, Dmax= 1.4e-02 nm, Epot= -4.55310e+04 Fmax= 1.21818e+02, atom= 1264\n",
      "Step=  466, Dmax= 8.7e-03 nm, Epot= -4.55335e+04 Fmax= 6.85399e+01, atom= 1264\n",
      "Step=  467, Dmax= 1.0e-02 nm, Epot= -4.55354e+04 Fmax= 1.71478e+02, atom= 1264\n",
      "Step=  468, Dmax= 1.3e-02 nm, Epot= -4.55386e+04 Fmax= 1.16256e+02, atom= 1264\n",
      "Step=  469, Dmax= 1.5e-02 nm, Epot= -4.55389e+04 Fmax= 2.28416e+02, atom= 1264\n",
      "Step=  470, Dmax= 1.8e-02 nm, Epot= -4.55423e+04 Fmax= 1.86440e+02, atom= 1264\n",
      "Step=  472, Dmax= 1.1e-02 nm, Epot= -4.55462e+04 Fmax= 6.65599e+01, atom= 5824\n",
      "Step=  473, Dmax= 1.3e-02 nm, Epot= -4.55479e+04 Fmax= 2.35647e+02, atom= 1264\n",
      "Step=  474, Dmax= 1.6e-02 nm, Epot= -4.55520e+04 Fmax= 1.32947e+02, atom= 1264\n",
      "Step=  476, Dmax= 9.3e-03 nm, Epot= -4.55546e+04 Fmax= 7.12243e+01, atom= 1264\n",
      "Step=  477, Dmax= 1.1e-02 nm, Epot= -4.55563e+04 Fmax= 1.88520e+02, atom= 1264\n",
      "Step=  478, Dmax= 1.3e-02 nm, Epot= -4.55597e+04 Fmax= 1.21857e+02, atom= 1264\n",
      "Step=  480, Dmax= 8.1e-03 nm, Epot= -4.55622e+04 Fmax= 6.11391e+01, atom= 1264\n",
      "Step=  481, Dmax= 9.7e-03 nm, Epot= -4.55645e+04 Fmax= 1.72616e+02, atom= 1264\n",
      "Step=  482, Dmax= 1.2e-02 nm, Epot= -4.55675e+04 Fmax= 9.73076e+01, atom= 1264\n",
      "Step=  483, Dmax= 1.4e-02 nm, Epot= -4.55682e+04 Fmax= 2.39947e+02, atom= 1264\n",
      "Step=  484, Dmax= 1.7e-02 nm, Epot= -4.55718e+04 Fmax= 1.48898e+02, atom= 1264\n",
      "Step=  486, Dmax= 1.0e-02 nm, Epot= -4.55746e+04 Fmax= 7.07733e+01, atom= 1264\n",
      "Step=  487, Dmax= 1.2e-02 nm, Epot= -4.55758e+04 Fmax= 2.11975e+02, atom= 1264\n",
      "Step=  488, Dmax= 1.4e-02 nm, Epot= -4.55797e+04 Fmax= 1.24149e+02, atom= 1264\n",
      "Step=  490, Dmax= 8.7e-03 nm, Epot= -4.55820e+04 Fmax= 7.05765e+01, atom= 1264\n",
      "Step=  491, Dmax= 1.0e-02 nm, Epot= -4.55838e+04 Fmax= 1.80952e+02, atom= 1264\n",
      "Step=  492, Dmax= 1.2e-02 nm, Epot= -4.55867e+04 Fmax= 1.08217e+02, atom= 1264\n",
      "Step=  493, Dmax= 1.5e-02 nm, Epot= -4.55869e+04 Fmax= 2.55069e+02, atom= 1264\n",
      "Step=  494, Dmax= 1.8e-02 nm, Epot= -4.55905e+04 Fmax= 1.62458e+02, atom= 1264\n",
      "Step=  496, Dmax= 1.1e-02 nm, Epot= -4.55934e+04 Fmax= 7.19876e+01, atom= 1264\n",
      "Step=  497, Dmax= 1.3e-02 nm, Epot= -4.55939e+04 Fmax= 2.33657e+02, atom= 1264\n",
      "Step=  498, Dmax= 1.6e-02 nm, Epot= -4.55982e+04 Fmax= 1.29079e+02, atom= 1264\n",
      "Step=  500, Dmax= 9.3e-03 nm, Epot= -4.56005e+04 Fmax= 7.82755e+01, atom= 1264\n",
      "Step=  501, Dmax= 1.1e-02 nm, Epot= -4.56017e+04 Fmax= 1.91028e+02, atom= 1264\n",
      "Step=  502, Dmax= 1.3e-02 nm, Epot= -4.56045e+04 Fmax= 1.17858e+02, atom= 1264\n",
      "Step=  504, Dmax= 8.1e-03 nm, Epot= -4.56067e+04 Fmax= 6.12183e+01, atom= 1264\n",
      "Step=  505, Dmax= 9.7e-03 nm, Epot= -4.56084e+04 Fmax= 1.57054e+02, atom= 1264\n",
      "Step=  506, Dmax= 1.2e-02 nm, Epot= -4.56109e+04 Fmax= 1.11038e+02, atom= 1264\n",
      "Step=  507, Dmax= 1.4e-02 nm, Epot= -4.56113e+04 Fmax= 2.02945e+02, atom= 1264\n",
      "Step=  508, Dmax= 1.7e-02 nm, Epot= -4.56137e+04 Fmax= 1.82632e+02, atom= 1264\n",
      "Step=  510, Dmax= 1.0e-02 nm, Epot= -4.56170e+04 Fmax= 5.44213e+01, atom= 5824\n",
      "Step=  511, Dmax= 1.2e-02 nm, Epot= -4.56188e+04 Fmax= 2.14129e+02, atom= 1264\n",
      "Step=  512, Dmax= 1.4e-02 nm, Epot= -4.56219e+04 Fmax= 1.22899e+02, atom= 1264\n",
      "Step=  514, Dmax= 8.7e-03 nm, Epot= -4.56240e+04 Fmax= 6.72173e+01, atom= 1264\n",
      "Step=  515, Dmax= 1.0e-02 nm, Epot= -4.56252e+04 Fmax= 1.68104e+02, atom= 1264\n",
      "Step=  516, Dmax= 1.2e-02 nm, Epot= -4.56278e+04 Fmax= 1.19144e+02, atom= 1264\n",
      "Step=  518, Dmax= 7.5e-03 nm, Epot= -4.56298e+04 Fmax= 5.14206e+01, atom= 5824\n",
      "Step=  519, Dmax= 9.0e-03 nm, Epot= -4.56316e+04 Fmax= 1.59831e+02, atom= 1264\n",
      "Step=  520, Dmax= 1.1e-02 nm, Epot= -4.56341e+04 Fmax= 8.75089e+01, atom= 1264\n",
      "Step=  521, Dmax= 1.3e-02 nm, Epot= -4.56341e+04 Fmax= 2.25079e+02, atom= 1264\n",
      "Step=  522, Dmax= 1.6e-02 nm, Epot= -4.56374e+04 Fmax= 1.31770e+02, atom= 1264\n",
      "Step=  524, Dmax= 9.3e-03 nm, Epot= -4.56396e+04 Fmax= 7.20213e+01, atom= 1264\n",
      "Step=  525, Dmax= 1.1e-02 nm, Epot= -4.56401e+04 Fmax= 1.81395e+02, atom= 1264\n",
      "Step=  526, Dmax= 1.3e-02 nm, Epot= -4.56429e+04 Fmax= 1.27643e+02, atom= 1264\n",
      "Step=  528, Dmax= 8.0e-03 nm, Epot= -4.56452e+04 Fmax= 5.65556e+01, atom= 5824\n",
      "Step=  529, Dmax= 9.6e-03 nm, Epot= -4.56462e+04 Fmax= 1.68386e+02, atom= 1264\n",
      "Step=  530, Dmax= 1.2e-02 nm, Epot= -4.56490e+04 Fmax= 9.67118e+01, atom= 1264\n",
      "Step=  532, Dmax= 6.9e-03 nm, Epot= -4.56508e+04 Fmax= 5.82563e+01, atom= 1264\n",
      "Step=  533, Dmax= 8.3e-03 nm, Epot= -4.56519e+04 Fmax= 1.26980e+02, atom= 1264\n",
      "Step=  534, Dmax= 1.0e-02 nm, Epot= -4.56539e+04 Fmax= 1.03427e+02, atom= 1264\n",
      "Step=  536, Dmax= 6.0e-03 nm, Epot= -4.56560e+04 Fmax= 3.59879e+01, atom= 582\n",
      "Step=  537, Dmax= 7.2e-03 nm, Epot= -4.56578e+04 Fmax= 1.31417e+02, atom= 626\n",
      "Step=  538, Dmax= 8.6e-03 nm, Epot= -4.56602e+04 Fmax= 7.34455e+01, atom= 626\n",
      "Step=  539, Dmax= 1.0e-02 nm, Epot= -4.56603e+04 Fmax= 1.73195e+02, atom= 626\n",
      "Step=  540, Dmax= 1.2e-02 nm, Epot= -4.56631e+04 Fmax= 1.21107e+02, atom= 626\n",
      "Step=  542, Dmax= 7.5e-03 nm, Epot= -4.56653e+04 Fmax= 5.14276e+01, atom= 626\n",
      "Step=  543, Dmax= 9.0e-03 nm, Epot= -4.56662e+04 Fmax= 1.71196e+02, atom= 626\n",
      "Step=  544, Dmax= 1.1e-02 nm, Epot= -4.56691e+04 Fmax= 8.82880e+01, atom= 626\n",
      "Step=  546, Dmax= 6.5e-03 nm, Epot= -4.56706e+04 Fmax= 6.41895e+01, atom= 626\n",
      "Step=  547, Dmax= 7.7e-03 nm, Epot= -4.56720e+04 Fmax= 1.17044e+02, atom= 626\n",
      "Step=  548, Dmax= 9.3e-03 nm, Epot= -4.56736e+04 Fmax= 1.02734e+02, atom= 626\n",
      "Step=  549, Dmax= 1.1e-02 nm, Epot= -4.56743e+04 Fmax= 1.61741e+02, atom= 626\n",
      "Step=  550, Dmax= 1.3e-02 nm, Epot= -4.56759e+04 Fmax= 1.54384e+02, atom= 626\n",
      "Step=  552, Dmax= 8.0e-03 nm, Epot= -4.56782e+04 Fmax= 3.38864e+01, atom= 111\n",
      "Step=  553, Dmax= 9.6e-03 nm, Epot= -4.56801e+04 Fmax= 2.14097e+02, atom= 626\n",
      "Step=  554, Dmax= 1.2e-02 nm, Epot= -4.56835e+04 Fmax= 7.52265e+01, atom= 626\n",
      "Step=  556, Dmax= 6.9e-03 nm, Epot= -4.56849e+04 Fmax= 8.64305e+01, atom= 626\n",
      "Step=  557, Dmax= 8.3e-03 nm, Epot= -4.56861e+04 Fmax= 1.08619e+02, atom= 626\n",
      "Step=  558, Dmax= 1.0e-02 nm, Epot= -4.56873e+04 Fmax= 1.27482e+02, atom= 626\n",
      "Step=  559, Dmax= 1.2e-02 nm, Epot= -4.56883e+04 Fmax= 1.56156e+02, atom= 626\n",
      "Step=  560, Dmax= 1.4e-02 nm, Epot= -4.56892e+04 Fmax= 1.83907e+02, atom= 626\n",
      "Step=  561, Dmax= 1.7e-02 nm, Epot= -4.56895e+04 Fmax= 2.29917e+02, atom= 626\n",
      "Step=  562, Dmax= 2.1e-02 nm, Epot= -4.56900e+04 Fmax= 2.59564e+02, atom= 626\n",
      "Step=  564, Dmax= 1.2e-02 nm, Epot= -4.56946e+04 Fmax= 4.79706e+01, atom= 111\n",
      "Step=  565, Dmax= 1.5e-02 nm, Epot= -4.56952e+04 Fmax= 2.71962e+02, atom= 626\n",
      "Step=  566, Dmax= 1.8e-02 nm, Epot= -4.56986e+04 Fmax= 1.97401e+02, atom= 626\n",
      "Step=  568, Dmax= 1.1e-02 nm, Epot= -4.57012e+04 Fmax= 5.53465e+01, atom= 339\n",
      "Step=  569, Dmax= 1.3e-02 nm, Epot= -4.57014e+04 Fmax= 2.54759e+02, atom= 339\n",
      "Step=  570, Dmax= 1.5e-02 nm, Epot= -4.57050e+04 Fmax= 1.19686e+02, atom= 626\n",
      "Step=  572, Dmax= 9.3e-03 nm, Epot= -4.57064e+04 Fmax= 8.76655e+01, atom= 626\n",
      "Step=  573, Dmax= 1.1e-02 nm, Epot= -4.57068e+04 Fmax= 1.81661e+02, atom= 626\n",
      "Step=  574, Dmax= 1.3e-02 nm, Epot= -4.57087e+04 Fmax= 1.36746e+02, atom= 626\n",
      "Step=  576, Dmax= 8.0e-03 nm, Epot= -4.57106e+04 Fmax= 5.28007e+01, atom= 626\n",
      "Step=  577, Dmax= 9.6e-03 nm, Epot= -4.57117e+04 Fmax= 1.71984e+02, atom= 626\n",
      "Step=  578, Dmax= 1.2e-02 nm, Epot= -4.57137e+04 Fmax= 1.01928e+02, atom= 626\n",
      "Step=  580, Dmax= 6.9e-03 nm, Epot= -4.57151e+04 Fmax= 5.67850e+01, atom= 626\n",
      "Step=  581, Dmax= 8.3e-03 nm, Epot= -4.57161e+04 Fmax= 1.45923e+02, atom= 626\n",
      "Step=  582, Dmax= 1.0e-02 nm, Epot= -4.57178e+04 Fmax= 9.20070e+01, atom= 626\n",
      "Step=  583, Dmax= 1.2e-02 nm, Epot= -4.57179e+04 Fmax= 1.95271e+02, atom= 626\n",
      "Step=  584, Dmax= 1.4e-02 nm, Epot= -4.57198e+04 Fmax= 1.49080e+02, atom= 626\n",
      "Step=  586, Dmax= 8.6e-03 nm, Epot= -4.57218e+04 Fmax= 5.45235e+01, atom= 626\n",
      "Step=  587, Dmax= 1.0e-02 nm, Epot= -4.57226e+04 Fmax= 1.90014e+02, atom= 626\n",
      "Step=  588, Dmax= 1.2e-02 nm, Epot= -4.57249e+04 Fmax= 1.05233e+02, atom= 626\n",
      "Step=  590, Dmax= 7.4e-03 nm, Epot= -4.57262e+04 Fmax= 6.50171e+01, atom= 626\n",
      "Step=  591, Dmax= 8.9e-03 nm, Epot= -4.57269e+04 Fmax= 1.51520e+02, atom= 626\n",
      "Step=  592, Dmax= 1.1e-02 nm, Epot= -4.57286e+04 Fmax= 1.04259e+02, atom= 626\n",
      "Step=  594, Dmax= 6.4e-03 nm, Epot= -4.57300e+04 Fmax= 4.86618e+01, atom= 626\n",
      "Step=  595, Dmax= 7.7e-03 nm, Epot= -4.57312e+04 Fmax= 1.31234e+02, atom= 626\n",
      "Step=  596, Dmax= 9.3e-03 nm, Epot= -4.57327e+04 Fmax= 8.79141e+01, atom= 626\n",
      "Step=  597, Dmax= 1.1e-02 nm, Epot= -4.57330e+04 Fmax= 1.77630e+02, atom= 626\n",
      "Step=  598, Dmax= 1.3e-02 nm, Epot= -4.57346e+04 Fmax= 1.37288e+02, atom= 626\n",
      "Step=  600, Dmax= 8.0e-03 nm, Epot= -4.57364e+04 Fmax= 4.65334e+01, atom= 626\n",
      "Step=  601, Dmax= 9.6e-03 nm, Epot= -4.57367e+04 Fmax= 1.97158e+02, atom= 626\n",
      "Step=  602, Dmax= 1.2e-02 nm, Epot= -4.57395e+04 Fmax= 8.53432e+01, atom= 626\n",
      "Step=  604, Dmax= 6.9e-03 nm, Epot= -4.57406e+04 Fmax= 7.80857e+01, atom= 626\n",
      "Step=  605, Dmax= 8.3e-03 nm, Epot= -4.57414e+04 Fmax= 1.17089e+02, atom= 626\n",
      "Step=  606, Dmax= 1.0e-02 nm, Epot= -4.57425e+04 Fmax= 1.18012e+02, atom= 626\n",
      "Step=  607, Dmax= 1.2e-02 nm, Epot= -4.57429e+04 Fmax= 1.66990e+02, atom= 626\n",
      "Step=  608, Dmax= 1.4e-02 nm, Epot= -4.57438e+04 Fmax= 1.71056e+02, atom= 626\n",
      "Step=  610, Dmax= 8.6e-03 nm, Epot= -4.57461e+04 Fmax= 3.25288e+01, atom= 111\n",
      "Step=  611, Dmax= 1.0e-02 nm, Epot= -4.57468e+04 Fmax= 2.21624e+02, atom= 626\n",
      "Step=  612, Dmax= 1.2e-02 nm, Epot= -4.57502e+04 Fmax= 9.43645e+01, atom= 626\n",
      "Step=  614, Dmax= 7.4e-03 nm, Epot= -4.57512e+04 Fmax= 7.85514e+01, atom= 626\n",
      "Step=  615, Dmax= 8.9e-03 nm, Epot= -4.57519e+04 Fmax= 1.32988e+02, atom= 626\n",
      "Step=  616, Dmax= 1.1e-02 nm, Epot= -4.57530e+04 Fmax= 1.19382e+02, atom= 626\n",
      "Step=  618, Dmax= 6.4e-03 nm, Epot= -4.57544e+04 Fmax= 2.94811e+01, atom= 626\n",
      "Step=  619, Dmax= 7.7e-03 nm, Epot= -4.57556e+04 Fmax= 1.67790e+02, atom= 626\n",
      "Step=  620, Dmax= 9.2e-03 nm, Epot= -4.57579e+04 Fmax= 5.88097e+01, atom= 626\n",
      "Step=  622, Dmax= 5.5e-03 nm, Epot= -4.57589e+04 Fmax= 7.25233e+01, atom= 626\n",
      "Step=  623, Dmax= 6.7e-03 nm, Epot= -4.57598e+04 Fmax= 8.45653e+01, atom= 626\n",
      "Step=  624, Dmax= 8.0e-03 nm, Epot= -4.57606e+04 Fmax= 1.04557e+02, atom= 626\n",
      "Step=  625, Dmax= 9.6e-03 nm, Epot= -4.57614e+04 Fmax= 1.23277e+02, atom= 626\n",
      "Step=  626, Dmax= 1.2e-02 nm, Epot= -4.57620e+04 Fmax= 1.48313e+02, atom= 626\n",
      "Step=  627, Dmax= 1.4e-02 nm, Epot= -4.57623e+04 Fmax= 1.83356e+02, atom= 626\n",
      "Step=  628, Dmax= 1.7e-02 nm, Epot= -4.57627e+04 Fmax= 2.06961e+02, atom= 626\n",
      "Step=  630, Dmax= 9.9e-03 nm, Epot= -4.57658e+04 Fmax= 3.36618e+01, atom= 111\n",
      "Step=  631, Dmax= 1.2e-02 nm, Epot= -4.57661e+04 Fmax= 2.32675e+02, atom= 626\n",
      "Step=  632, Dmax= 1.4e-02 nm, Epot= -4.57693e+04 Fmax= 1.43688e+02, atom= 626\n",
      "Step=  634, Dmax= 8.6e-03 nm, Epot= -4.57709e+04 Fmax= 5.70110e+01, atom= 626\n",
      "Step=  636, Dmax= 5.2e-03 nm, Epot= -4.57718e+04 Fmax= 6.27797e+01, atom= 626\n",
      "Step=  637, Dmax= 6.2e-03 nm, Epot= -4.57727e+04 Fmax= 8.34530e+01, atom= 626\n",
      "Step=  638, Dmax= 7.4e-03 nm, Epot= -4.57735e+04 Fmax= 9.19966e+01, atom= 626\n",
      "Step=  639, Dmax= 8.9e-03 nm, Epot= -4.57742e+04 Fmax= 1.18256e+02, atom= 626\n",
      "Step=  640, Dmax= 1.1e-02 nm, Epot= -4.57749e+04 Fmax= 1.36731e+02, atom= 626\n",
      "Step=  641, Dmax= 1.3e-02 nm, Epot= -4.57753e+04 Fmax= 1.65361e+02, atom= 626\n",
      "Step=  642, Dmax= 1.5e-02 nm, Epot= -4.57754e+04 Fmax= 2.05899e+02, atom= 626\n",
      "Step=  643, Dmax= 1.8e-02 nm, Epot= -4.57756e+04 Fmax= 2.28102e+02, atom= 626\n",
      "Step=  645, Dmax= 1.1e-02 nm, Epot= -4.57794e+04 Fmax= 4.02938e+01, atom= 111\n",
      "Step=  647, Dmax= 6.6e-03 nm, Epot= -4.57805e+04 Fmax= 1.02959e+02, atom= 626\n",
      "Step=  648, Dmax= 8.0e-03 nm, Epot= -4.57815e+04 Fmax= 9.19483e+01, atom= 626\n",
      "Step=  649, Dmax= 9.6e-03 nm, Epot= -4.57820e+04 Fmax= 1.32794e+02, atom= 626\n",
      "Step=  650, Dmax= 1.1e-02 nm, Epot= -4.57827e+04 Fmax= 1.41105e+02, atom= 626\n",
      "Step=  651, Dmax= 1.4e-02 nm, Epot= -4.57829e+04 Fmax= 1.82665e+02, atom= 626\n",
      "Step=  652, Dmax= 1.7e-02 nm, Epot= -4.57830e+04 Fmax= 2.16710e+02, atom= 626\n",
      "Step=  654, Dmax= 9.9e-03 nm, Epot= -4.57864e+04 Fmax= 2.30861e+01, atom= 339\n",
      "Step=  655, Dmax= 1.2e-02 nm, Epot= -4.57890e+04 Fmax= 2.47514e+02, atom= 339\n",
      "Step=  656, Dmax= 1.4e-02 nm, Epot= -4.57916e+04 Fmax= 9.66893e+01, atom= 339\n",
      "Step=  658, Dmax= 8.6e-03 nm, Epot= -4.57924e+04 Fmax= 1.12369e+02, atom= 339\n",
      "Step=  659, Dmax= 1.0e-02 nm, Epot= -4.57930e+04 Fmax= 1.27581e+02, atom= 626\n",
      "Step=  660, Dmax= 1.2e-02 nm, Epot= -4.57933e+04 Fmax= 1.70183e+02, atom= 339\n",
      "Step=  661, Dmax= 1.5e-02 nm, Epot= -4.57939e+04 Fmax= 1.76601e+02, atom= 339\n",
      "Step=  663, Dmax= 8.9e-03 nm, Epot= -4.57963e+04 Fmax= 3.23171e+01, atom= 111\n",
      "Step=  665, Dmax= 5.3e-03 nm, Epot= -4.57974e+04 Fmax= 9.66383e+01, atom= 339\n",
      "Step=  666, Dmax= 6.4e-03 nm, Epot= -4.57985e+04 Fmax= 5.82051e+01, atom= 626\n",
      "Step=  667, Dmax= 7.7e-03 nm, Epot= -4.57991e+04 Fmax= 1.21677e+02, atom= 339\n",
      "Step=  668, Dmax= 9.2e-03 nm, Epot= -4.58002e+04 Fmax= 9.81286e+01, atom= 339\n",
      "Step=  669, Dmax= 1.1e-02 nm, Epot= -4.58003e+04 Fmax= 1.62097e+02, atom= 339\n",
      "Step=  670, Dmax= 1.3e-02 nm, Epot= -4.58012e+04 Fmax= 1.57590e+02, atom= 339\n",
      "Step=  672, Dmax= 8.0e-03 nm, Epot= -4.58033e+04 Fmax= 3.24485e+01, atom= 339\n",
      "Step=  673, Dmax= 9.6e-03 nm, Epot= -4.58044e+04 Fmax= 1.91130e+02, atom= 339\n",
      "Step=  674, Dmax= 1.1e-02 nm, Epot= -4.58066e+04 Fmax= 8.07609e+01, atom= 339\n",
      "Step=  676, Dmax= 6.9e-03 nm, Epot= -4.58074e+04 Fmax= 7.90443e+01, atom= 339\n",
      "Step=  677, Dmax= 8.3e-03 nm, Epot= -4.58080e+04 Fmax= 1.14352e+02, atom= 339\n",
      "Step=  678, Dmax= 9.9e-03 nm, Epot= -4.58088e+04 Fmax= 1.21477e+02, atom= 339\n",
      "Step=  679, Dmax= 1.2e-02 nm, Epot= -4.58091e+04 Fmax= 1.56905e+02, atom= 339\n",
      "Step=  680, Dmax= 1.4e-02 nm, Epot= -4.58095e+04 Fmax= 1.86347e+02, atom= 339\n",
      "Step=  681, Dmax= 1.7e-02 nm, Epot= -4.58096e+04 Fmax= 2.13906e+02, atom= 339\n",
      "Step=  683, Dmax= 1.0e-02 nm, Epot= -4.58130e+04 Fmax= 3.28962e+01, atom= 111\n",
      "Step=  685, Dmax= 6.2e-03 nm, Epot= -4.58142e+04 Fmax= 1.00185e+02, atom= 339\n",
      "Step=  686, Dmax= 7.4e-03 nm, Epot= -4.58153e+04 Fmax= 8.16074e+01, atom= 339\n",
      "Step=  687, Dmax= 8.9e-03 nm, Epot= -4.58158e+04 Fmax= 1.25340e+02, atom= 339\n",
      "Step=  688, Dmax= 1.1e-02 nm, Epot= -4.58166e+04 Fmax= 1.28269e+02, atom= 339\n",
      "Step=  689, Dmax= 1.3e-02 nm, Epot= -4.58168e+04 Fmax= 1.70713e+02, atom= 339\n",
      "Step=  690, Dmax= 1.5e-02 nm, Epot= -4.58171e+04 Fmax= 1.98108e+02, atom= 339\n",
      "Step=  692, Dmax= 9.2e-03 nm, Epot= -4.58200e+04 Fmax= 2.29123e+01, atom= 339\n",
      "Step=  693, Dmax= 1.1e-02 nm, Epot= -4.58226e+04 Fmax= 2.23666e+02, atom= 339\n",
      "Step=  694, Dmax= 1.3e-02 nm, Epot= -4.58249e+04 Fmax= 9.22479e+01, atom= 339\n",
      "Step=  696, Dmax= 7.9e-03 nm, Epot= -4.58257e+04 Fmax= 9.87011e+01, atom= 339\n",
      "Step=  697, Dmax= 9.5e-03 nm, Epot= -4.58264e+04 Fmax= 1.22014e+02, atom= 339\n",
      "Step=  698, Dmax= 1.1e-02 nm, Epot= -4.58268e+04 Fmax= 1.51478e+02, atom= 339\n",
      "Step=  699, Dmax= 1.4e-02 nm, Epot= -4.58274e+04 Fmax= 1.68389e+02, atom= 339\n",
      "Step=  701, Dmax= 8.2e-03 nm, Epot= -4.58296e+04 Fmax= 2.49104e+01, atom= 111\n",
      "Step=  702, Dmax= 9.9e-03 nm, Epot= -4.58302e+04 Fmax= 2.22306e+02, atom= 339\n",
      "Step=  703, Dmax= 1.2e-02 nm, Epot= -4.58338e+04 Fmax= 8.38243e+01, atom= 339\n",
      "Step=  705, Dmax= 7.1e-03 nm, Epot= -4.58347e+04 Fmax= 7.97399e+01, atom= 339\n",
      "Step=  706, Dmax= 8.5e-03 nm, Epot= -4.58353e+04 Fmax= 1.22699e+02, atom= 339\n",
      "Step=  707, Dmax= 1.0e-02 nm, Epot= -4.58362e+04 Fmax= 1.16140e+02, atom= 339\n",
      "Step=  708, Dmax= 1.2e-02 nm, Epot= -4.58362e+04 Fmax= 1.77221e+02, atom= 339\n",
      "Step=  709, Dmax= 1.5e-02 nm, Epot= -4.58372e+04 Fmax= 1.65875e+02, atom= 339\n",
      "Step=  711, Dmax= 8.9e-03 nm, Epot= -4.58394e+04 Fmax= 3.68963e+01, atom= 339\n",
      "Step=  713, Dmax= 5.3e-03 nm, Epot= -4.58404e+04 Fmax= 9.72060e+01, atom= 339\n",
      "Step=  714, Dmax= 6.4e-03 nm, Epot= -4.58415e+04 Fmax= 5.42322e+01, atom= 339\n",
      "Step=  715, Dmax= 7.7e-03 nm, Epot= -4.58422e+04 Fmax= 1.25504e+02, atom= 339\n",
      "Step=  716, Dmax= 9.2e-03 nm, Epot= -4.58434e+04 Fmax= 9.14520e+01, atom= 339\n",
      "Step=  717, Dmax= 1.1e-02 nm, Epot= -4.58435e+04 Fmax= 1.66624e+02, atom= 339\n",
      "Step=  718, Dmax= 1.3e-02 nm, Epot= -4.58447e+04 Fmax= 1.48350e+02, atom= 339\n",
      "Step=  720, Dmax= 7.9e-03 nm, Epot= -4.58466e+04 Fmax= 3.86064e+01, atom= 339\n",
      "Step=  721, Dmax= 9.5e-03 nm, Epot= -4.58475e+04 Fmax= 1.82197e+02, atom= 339\n",
      "Step=  722, Dmax= 1.1e-02 nm, Epot= -4.58495e+04 Fmax= 8.70904e+01, atom= 339\n",
      "Step=  724, Dmax= 6.9e-03 nm, Epot= -4.58505e+04 Fmax= 7.01013e+01, atom= 339\n",
      "Step=  725, Dmax= 8.2e-03 nm, Epot= -4.58512e+04 Fmax= 1.22960e+02, atom= 339\n",
      "Step=  726, Dmax= 9.9e-03 nm, Epot= -4.58523e+04 Fmax= 1.09954e+02, atom= 339\n",
      "Step=  727, Dmax= 1.2e-02 nm, Epot= -4.58525e+04 Fmax= 1.65851e+02, atom= 339\n",
      "Step=  728, Dmax= 1.4e-02 nm, Epot= -4.58533e+04 Fmax= 1.72371e+02, atom= 339\n",
      "Step=  730, Dmax= 8.5e-03 nm, Epot= -4.58557e+04 Fmax= 2.92063e+01, atom= 626\n",
      "Step=  731, Dmax= 1.0e-02 nm, Epot= -4.58575e+04 Fmax= 2.06424e+02, atom= 339\n",
      "Step=  732, Dmax= 1.2e-02 nm, Epot= -4.58599e+04 Fmax= 8.49054e+01, atom= 339\n",
      "Step=  734, Dmax= 7.4e-03 nm, Epot= -4.58609e+04 Fmax= 8.57352e+01, atom= 339\n",
      "Step=  735, Dmax= 8.8e-03 nm, Epot= -4.58617e+04 Fmax= 1.18904e+02, atom= 339\n",
      "Step=  736, Dmax= 1.1e-02 nm, Epot= -4.58626e+04 Fmax= 1.30971e+02, atom= 339\n",
      "Step=  737, Dmax= 1.3e-02 nm, Epot= -4.58631e+04 Fmax= 1.64207e+02, atom= 339\n",
      "Step=  738, Dmax= 1.5e-02 nm, Epot= -4.58634e+04 Fmax= 1.99393e+02, atom= 339\n",
      "Step=  739, Dmax= 1.8e-02 nm, Epot= -4.58637e+04 Fmax= 2.24656e+02, atom= 339\n",
      "Step=  741, Dmax= 1.1e-02 nm, Epot= -4.58674e+04 Fmax= 3.67078e+01, atom= 373\n",
      "Step=  743, Dmax= 6.6e-03 nm, Epot= -4.58688e+04 Fmax= 1.08037e+02, atom= 339\n",
      "Step=  744, Dmax= 7.9e-03 nm, Epot= -4.58701e+04 Fmax= 8.31847e+01, atom= 339\n",
      "Step=  745, Dmax= 9.5e-03 nm, Epot= -4.58708e+04 Fmax= 1.36275e+02, atom= 339\n",
      "Step=  746, Dmax= 1.1e-02 nm, Epot= -4.58718e+04 Fmax= 1.31440e+02, atom= 339\n",
      "Step=  747, Dmax= 1.4e-02 nm, Epot= -4.58720e+04 Fmax= 1.86017e+02, atom= 339\n",
      "Step=  748, Dmax= 1.6e-02 nm, Epot= -4.58727e+04 Fmax= 2.04077e+02, atom= 339\n",
      "Step=  750, Dmax= 9.9e-03 nm, Epot= -4.58758e+04 Fmax= 3.01696e+01, atom= 626\n",
      "Step=  751, Dmax= 1.2e-02 nm, Epot= -4.58782e+04 Fmax= 2.29559e+02, atom= 626\n",
      "Step=  752, Dmax= 1.4e-02 nm, Epot= -4.58808e+04 Fmax= 1.07844e+02, atom= 339\n",
      "Step=  754, Dmax= 8.5e-03 nm, Epot= -4.58820e+04 Fmax= 8.79604e+01, atom= 339\n",
      "Step=  755, Dmax= 1.0e-02 nm, Epot= -4.58826e+04 Fmax= 1.49108e+02, atom= 339\n",
      "Step=  756, Dmax= 1.2e-02 nm, Epot= -4.58838e+04 Fmax= 1.38957e+02, atom= 339\n",
      "Step=  757, Dmax= 1.5e-02 nm, Epot= -4.58838e+04 Fmax= 2.02099e+02, atom= 339\n",
      "Step=  758, Dmax= 1.8e-02 nm, Epot= -4.58845e+04 Fmax= 2.17486e+02, atom= 339\n",
      "Step=  760, Dmax= 1.1e-02 nm, Epot= -4.58880e+04 Fmax= 3.34163e+01, atom= 626\n",
      "Step=  761, Dmax= 1.3e-02 nm, Epot= -4.58900e+04 Fmax= 2.47808e+02, atom= 626\n",
      "Step=  762, Dmax= 1.5e-02 nm, Epot= -4.58930e+04 Fmax= 1.16214e+02, atom= 339\n",
      "Step=  764, Dmax= 9.2e-03 nm, Epot= -4.58942e+04 Fmax= 9.36903e+01, atom= 339\n",
      "Step=  765, Dmax= 1.1e-02 nm, Epot= -4.58947e+04 Fmax= 1.61052e+02, atom= 339\n",
      "Step=  766, Dmax= 1.3e-02 nm, Epot= -4.58960e+04 Fmax= 1.47897e+02, atom= 339\n",
      "Step=  768, Dmax= 7.9e-03 nm, Epot= -4.58980e+04 Fmax= 3.58704e+01, atom= 626\n",
      "Step=  769, Dmax= 9.5e-03 nm, Epot= -4.58997e+04 Fmax= 1.83300e+02, atom= 339\n",
      "Step=  770, Dmax= 1.1e-02 nm, Epot= -4.59019e+04 Fmax= 8.29662e+01, atom= 339\n",
      "Step=  772, Dmax= 6.8e-03 nm, Epot= -4.59031e+04 Fmax= 7.23602e+01, atom= 339\n",
      "Step=  773, Dmax= 8.2e-03 nm, Epot= -4.59041e+04 Fmax= 1.17845e+02, atom= 339\n",
      "Step=  774, Dmax= 9.8e-03 nm, Epot= -4.59053e+04 Fmax= 1.11226e+02, atom= 339\n",
      "Step=  775, Dmax= 1.2e-02 nm, Epot= -4.59059e+04 Fmax= 1.61287e+02, atom= 339\n",
      "Step=  776, Dmax= 1.4e-02 nm, Epot= -4.59068e+04 Fmax= 1.70512e+02, atom= 339\n",
      "Step=  777, Dmax= 1.7e-02 nm, Epot= -4.59069e+04 Fmax= 2.21020e+02, atom= 339\n",
      "Step=  778, Dmax= 2.0e-02 nm, Epot= -4.59070e+04 Fmax= 2.63265e+02, atom= 339\n",
      "Step=  780, Dmax= 1.2e-02 nm, Epot= -4.59118e+04 Fmax= 2.87628e+01, atom= 626\n",
      "Step=  781, Dmax= 1.5e-02 nm, Epot= -4.59154e+04 Fmax= 2.75397e+02, atom= 626\n",
      "Step=  782, Dmax= 1.8e-02 nm, Epot= -4.59182e+04 Fmax= 1.44366e+02, atom= 339\n",
      "Step=  784, Dmax= 1.1e-02 nm, Epot= -4.59197e+04 Fmax= 1.03991e+02, atom= 339\n",
      "Step=  785, Dmax= 1.3e-02 nm, Epot= -4.59198e+04 Fmax= 1.88353e+02, atom= 339\n",
      "Step=  786, Dmax= 1.5e-02 nm, Epot= -4.59213e+04 Fmax= 1.68242e+02, atom= 339\n",
      "Step=  788, Dmax= 9.1e-03 nm, Epot= -4.59236e+04 Fmax= 4.25005e+01, atom= 626\n",
      "Step=  789, Dmax= 1.1e-02 nm, Epot= -4.59247e+04 Fmax= 2.08891e+02, atom= 339\n",
      "Step=  790, Dmax= 1.3e-02 nm, Epot= -4.59273e+04 Fmax= 9.82721e+01, atom= 339\n",
      "Step=  792, Dmax= 7.9e-03 nm, Epot= -4.59285e+04 Fmax= 7.88287e+01, atom= 339\n",
      "Step=  793, Dmax= 9.5e-03 nm, Epot= -4.59292e+04 Fmax= 1.40228e+02, atom= 339\n",
      "Step=  794, Dmax= 1.1e-02 nm, Epot= -4.59305e+04 Fmax= 1.23526e+02, atom= 339\n",
      "Step=  795, Dmax= 1.4e-02 nm, Epot= -4.59306e+04 Fmax= 1.90196e+02, atom= 339\n",
      "Step=  796, Dmax= 1.6e-02 nm, Epot= -4.59316e+04 Fmax= 1.92276e+02, atom= 339\n",
      "Step=  798, Dmax= 9.8e-03 nm, Epot= -4.59345e+04 Fmax= 3.59415e+01, atom= 626\n",
      "Step=  799, Dmax= 1.2e-02 nm, Epot= -4.59361e+04 Fmax= 2.22986e+02, atom= 626\n",
      "Step=  800, Dmax= 1.4e-02 nm, Epot= -4.59388e+04 Fmax= 1.08835e+02, atom= 339\n",
      "Step=  802, Dmax= 8.5e-03 nm, Epot= -4.59400e+04 Fmax= 8.22214e+01, atom= 339\n",
      "Step=  803, Dmax= 1.0e-02 nm, Epot= -4.59405e+04 Fmax= 1.52607e+02, atom= 339\n",
      "Step=  804, Dmax= 1.2e-02 nm, Epot= -4.59419e+04 Fmax= 1.30530e+02, atom= 339\n",
      "Step=  806, Dmax= 7.3e-03 nm, Epot= -4.59436e+04 Fmax= 3.69766e+01, atom= 339\n",
      "Step=  807, Dmax= 8.8e-03 nm, Epot= -4.59450e+04 Fmax= 1.64574e+02, atom= 339\n",
      "Step=  808, Dmax= 1.1e-02 nm, Epot= -4.59470e+04 Fmax= 7.84499e+01, atom= 339\n",
      "Step=  810, Dmax= 6.3e-03 nm, Epot= -4.59481e+04 Fmax= 6.38636e+01, atom= 339\n",
      "Step=  811, Dmax= 7.6e-03 nm, Epot= -4.59490e+04 Fmax= 1.10600e+02, atom= 339\n",
      "Step=  812, Dmax= 9.1e-03 nm, Epot= -4.59502e+04 Fmax= 9.94042e+01, atom= 339\n",
      "Step=  813, Dmax= 1.1e-02 nm, Epot= -4.59508e+04 Fmax= 1.50806e+02, atom= 339\n",
      "Step=  814, Dmax= 1.3e-02 nm, Epot= -4.59518e+04 Fmax= 1.53324e+02, atom= 339\n",
      "Step=  815, Dmax= 1.6e-02 nm, Epot= -4.59519e+04 Fmax= 2.06270e+02, atom= 339\n",
      "Step=  816, Dmax= 1.9e-02 nm, Epot= -4.59522e+04 Fmax= 2.35618e+02, atom= 339\n",
      "Step=  818, Dmax= 1.1e-02 nm, Epot= -4.59562e+04 Fmax= 3.07404e+01, atom= 626\n",
      "Step=  819, Dmax= 1.4e-02 nm, Epot= -4.59589e+04 Fmax= 2.49983e+02, atom= 626\n",
      "Step=  820, Dmax= 1.6e-02 nm, Epot= -4.59615e+04 Fmax= 1.31232e+02, atom= 339\n",
      "Step=  822, Dmax= 9.8e-03 nm, Epot= -4.59629e+04 Fmax= 9.17377e+01, atom= 339\n",
      "Step=  823, Dmax= 1.2e-02 nm, Epot= -4.59630e+04 Fmax= 1.78002e+02, atom= 339\n",
      "Step=  824, Dmax= 1.4e-02 nm, Epot= -4.59645e+04 Fmax= 1.47893e+02, atom= 339\n",
      "Step=  826, Dmax= 8.5e-03 nm, Epot= -4.59665e+04 Fmax= 4.37481e+01, atom= 626\n",
      "Step=  827, Dmax= 1.0e-02 nm, Epot= -4.59674e+04 Fmax= 1.88920e+02, atom= 339\n",
      "Step=  828, Dmax= 1.2e-02 nm, Epot= -4.59697e+04 Fmax= 9.13859e+01, atom= 339\n",
      "Step=  830, Dmax= 7.3e-03 nm, Epot= -4.59708e+04 Fmax= 7.08268e+01, atom= 339\n",
      "Step=  831, Dmax= 8.8e-03 nm, Epot= -4.59716e+04 Fmax= 1.30459e+02, atom= 339\n",
      "Step=  832, Dmax= 1.1e-02 nm, Epot= -4.59729e+04 Fmax= 1.10408e+02, atom= 339\n",
      "Step=  833, Dmax= 1.3e-02 nm, Epot= -4.59731e+04 Fmax= 1.76787e+02, atom= 339\n",
      "Step=  834, Dmax= 1.5e-02 nm, Epot= -4.59743e+04 Fmax= 1.72232e+02, atom= 339\n",
      "Step=  836, Dmax= 9.1e-03 nm, Epot= -4.59767e+04 Fmax= 3.56087e+01, atom= 626\n",
      "Step=  837, Dmax= 1.1e-02 nm, Epot= -4.59783e+04 Fmax= 2.02562e+02, atom= 339\n",
      "Step=  838, Dmax= 1.3e-02 nm, Epot= -4.59807e+04 Fmax= 1.00461e+02, atom= 339\n",
      "Step=  840, Dmax= 7.9e-03 nm, Epot= -4.59820e+04 Fmax= 7.41119e+01, atom= 339\n",
      "Step=  841, Dmax= 9.4e-03 nm, Epot= -4.59826e+04 Fmax= 1.40962e+02, atom= 339\n",
      "Step=  842, Dmax= 1.1e-02 nm, Epot= -4.59840e+04 Fmax= 1.17473e+02, atom= 339\n",
      "Step=  843, Dmax= 1.4e-02 nm, Epot= -4.59841e+04 Fmax= 1.90774e+02, atom= 339\n",
      "Step=  844, Dmax= 1.6e-02 nm, Epot= -4.59852e+04 Fmax= 1.83520e+02, atom= 339\n",
      "Step=  846, Dmax= 9.8e-03 nm, Epot= -4.59879e+04 Fmax= 3.89524e+01, atom= 626\n",
      "Step=  847, Dmax= 1.2e-02 nm, Epot= -4.59892e+04 Fmax= 2.14554e+02, atom= 626\n",
      "Step=  848, Dmax= 1.4e-02 nm, Epot= -4.59918e+04 Fmax= 1.09660e+02, atom= 339\n",
      "Step=  850, Dmax= 8.5e-03 nm, Epot= -4.59931e+04 Fmax= 7.67259e+01, atom= 339\n",
      "Step=  851, Dmax= 1.0e-02 nm, Epot= -4.59936e+04 Fmax= 1.54610e+02, atom= 339\n",
      "Step=  852, Dmax= 1.2e-02 nm, Epot= -4.59951e+04 Fmax= 1.22581e+02, atom= 339\n",
      "Step=  854, Dmax= 7.3e-03 nm, Epot= -4.59967e+04 Fmax= 4.02329e+01, atom= 339\n",
      "Step=  855, Dmax= 8.8e-03 nm, Epot= -4.59980e+04 Fmax= 1.57835e+02, atom= 339\n",
      "Step=  856, Dmax= 1.1e-02 nm, Epot= -4.59999e+04 Fmax= 7.94969e+01, atom= 339\n",
      "Step=  858, Dmax= 6.3e-03 nm, Epot= -4.60010e+04 Fmax= 5.93191e+01, atom= 339\n",
      "Step=  859, Dmax= 7.6e-03 nm, Epot= -4.60020e+04 Fmax= 1.12260e+02, atom= 339\n",
      "Step=  860, Dmax= 9.1e-03 nm, Epot= -4.60032e+04 Fmax= 9.29688e+01, atom= 339\n",
      "Step=  861, Dmax= 1.1e-02 nm, Epot= -4.60037e+04 Fmax= 1.52243e+02, atom= 339\n",
      "Step=  862, Dmax= 1.3e-02 nm, Epot= -4.60049e+04 Fmax= 1.44542e+02, atom= 339\n",
      "Step=  864, Dmax= 7.9e-03 nm, Epot= -4.60067e+04 Fmax= 3.12378e+01, atom= 626\n",
      "Step=  865, Dmax= 9.4e-03 nm, Epot= -4.60086e+04 Fmax= 1.74690e+02, atom= 339\n",
      "Step=  866, Dmax= 1.1e-02 nm, Epot= -4.60107e+04 Fmax= 8.15345e+01, atom= 339\n",
      "Step=  868, Dmax= 6.8e-03 nm, Epot= -4.60118e+04 Fmax= 6.76013e+01, atom= 339\n",
      "Step=  869, Dmax= 8.1e-03 nm, Epot= -4.60127e+04 Fmax= 1.15008e+02, atom= 339\n",
      "Step=  870, Dmax= 9.8e-03 nm, Epot= -4.60138e+04 Fmax= 1.04545e+02, atom= 339\n",
      "Step=  871, Dmax= 1.2e-02 nm, Epot= -4.60143e+04 Fmax= 1.57190e+02, atom= 339\n",
      "Step=  872, Dmax= 1.4e-02 nm, Epot= -4.60153e+04 Fmax= 1.59444e+02, atom= 339\n",
      "Step=  874, Dmax= 8.4e-03 nm, Epot= -4.60175e+04 Fmax= 2.95869e+01, atom= 626\n",
      "Step=  875, Dmax= 1.0e-02 nm, Epot= -4.60195e+04 Fmax= 1.82758e+02, atom= 626\n",
      "Step=  876, Dmax= 1.2e-02 nm, Epot= -4.60217e+04 Fmax= 9.26096e+01, atom= 339\n",
      "Step=  878, Dmax= 7.3e-03 nm, Epot= -4.60228e+04 Fmax= 6.74876e+01, atom= 339\n",
      "Step=  879, Dmax= 8.8e-03 nm, Epot= -4.60236e+04 Fmax= 1.28510e+02, atom= 339\n",
      "Step=  880, Dmax= 1.1e-02 nm, Epot= -4.60248e+04 Fmax= 1.06742e+02, atom= 339\n",
      "Step=  881, Dmax= 1.3e-02 nm, Epot= -4.60250e+04 Fmax= 1.73983e+02, atom= 339\n",
      "Step=  882, Dmax= 1.5e-02 nm, Epot= -4.60261e+04 Fmax= 1.64498e+02, atom= 339\n",
      "Step=  884, Dmax= 9.1e-03 nm, Epot= -4.60284e+04 Fmax= 3.65172e+01, atom= 626\n",
      "Step=  885, Dmax= 1.1e-02 nm, Epot= -4.60296e+04 Fmax= 1.93786e+02, atom= 626\n",
      "Step=  886, Dmax= 1.3e-02 nm, Epot= -4.60320e+04 Fmax= 1.00589e+02, atom= 339\n",
      "Step=  888, Dmax= 7.8e-03 nm, Epot= -4.60332e+04 Fmax= 6.96189e+01, atom= 339\n",
      "Step=  889, Dmax= 9.4e-03 nm, Epot= -4.60338e+04 Fmax= 1.40895e+02, atom= 339\n",
      "Step=  890, Dmax= 1.1e-02 nm, Epot= -4.60351e+04 Fmax= 1.09929e+02, atom= 339\n",
      "Step=  892, Dmax= 6.8e-03 nm, Epot= -4.60365e+04 Fmax= 3.78470e+01, atom= 339\n",
      "Step=  893, Dmax= 8.1e-03 nm, Epot= -4.60377e+04 Fmax= 1.40660e+02, atom= 339\n",
      "Step=  894, Dmax= 9.8e-03 nm, Epot= -4.60393e+04 Fmax= 7.44084e+01, atom= 339\n",
      "Step=  896, Dmax= 5.9e-03 nm, Epot= -4.60404e+04 Fmax= 5.29986e+01, atom= 339\n",
      "Step=  897, Dmax= 7.0e-03 nm, Epot= -4.60413e+04 Fmax= 1.03341e+02, atom= 339\n",
      "Step=  898, Dmax= 8.4e-03 nm, Epot= -4.60424e+04 Fmax= 8.34452e+01, atom= 339\n",
      "Step=  899, Dmax= 1.0e-02 nm, Epot= -4.60430e+04 Fmax= 1.40299e+02, atom= 339\n",
      "Step=  900, Dmax= 1.2e-02 nm, Epot= -4.60441e+04 Fmax= 1.27627e+02, atom= 339\n",
      "Step=  902, Dmax= 7.3e-03 nm, Epot= -4.60457e+04 Fmax= 3.10242e+01, atom= 626\n",
      "Step=  903, Dmax= 8.7e-03 nm, Epot= -4.60472e+04 Fmax= 1.59598e+02, atom= 339\n",
      "Step=  904, Dmax= 1.0e-02 nm, Epot= -4.60491e+04 Fmax= 7.32902e+01, atom= 339\n",
      "Step=  906, Dmax= 6.3e-03 nm, Epot= -4.60501e+04 Fmax= 6.22260e+01, atom= 339\n",
      "Step=  907, Dmax= 7.6e-03 nm, Epot= -4.60509e+04 Fmax= 1.04430e+02, atom= 339\n",
      "Step=  908, Dmax= 9.1e-03 nm, Epot= -4.60519e+04 Fmax= 9.36935e+01, atom= 339\n",
      "Step=  909, Dmax= 1.1e-02 nm, Epot= -4.60524e+04 Fmax= 1.45083e+02, atom= 339\n",
      "Step=  910, Dmax= 1.3e-02 nm, Epot= -4.60533e+04 Fmax= 1.42734e+02, atom= 339\n",
      "Step=  912, Dmax= 7.8e-03 nm, Epot= -4.60551e+04 Fmax= 2.79819e+01, atom= 626\n",
      "Step=  913, Dmax= 9.4e-03 nm, Epot= -4.60567e+04 Fmax= 1.69572e+02, atom= 339\n",
      "Step=  914, Dmax= 1.1e-02 nm, Epot= -4.60587e+04 Fmax= 8.09347e+01, atom= 339\n",
      "Step=  916, Dmax= 6.8e-03 nm, Epot= -4.60596e+04 Fmax= 6.40327e+01, atom= 339\n",
      "Step=  917, Dmax= 8.1e-03 nm, Epot= -4.60603e+04 Fmax= 1.14264e+02, atom= 339\n",
      "Step=  918, Dmax= 9.7e-03 nm, Epot= -4.60613e+04 Fmax= 9.81419e+01, atom= 339\n",
      "Step=  919, Dmax= 1.2e-02 nm, Epot= -4.60614e+04 Fmax= 1.57401e+02, atom= 339\n",
      "Step=  920, Dmax= 1.4e-02 nm, Epot= -4.60623e+04 Fmax= 1.50803e+02, atom= 339\n",
      "Step=  922, Dmax= 8.4e-03 nm, Epot= -4.60642e+04 Fmax= 3.15662e+01, atom= 626\n",
      "Step=  923, Dmax= 1.0e-02 nm, Epot= -4.60652e+04 Fmax= 1.80039e+02, atom= 339\n",
      "Step=  924, Dmax= 1.2e-02 nm, Epot= -4.60673e+04 Fmax= 8.82780e+01, atom= 339\n",
      "Step=  926, Dmax= 7.3e-03 nm, Epot= -4.60682e+04 Fmax= 6.53041e+01, atom= 339\n",
      "Step=  927, Dmax= 8.7e-03 nm, Epot= -4.60686e+04 Fmax= 1.26425e+02, atom= 339\n",
      "Step=  928, Dmax= 1.0e-02 nm, Epot= -4.60697e+04 Fmax= 1.01643e+02, atom= 339\n",
      "Step=  930, Dmax= 6.3e-03 nm, Epot= -4.60708e+04 Fmax= 3.34565e+01, atom= 339\n",
      "Step=  931, Dmax= 7.5e-03 nm, Epot= -4.60716e+04 Fmax= 1.28651e+02, atom= 339\n",
      "Step=  932, Dmax= 9.1e-03 nm, Epot= -4.60731e+04 Fmax= 6.67952e+01, atom= 339\n",
      "Step=  934, Dmax= 5.4e-03 nm, Epot= -4.60739e+04 Fmax= 4.89232e+01, atom= 339\n",
      "Step=  935, Dmax= 6.5e-03 nm, Epot= -4.60745e+04 Fmax= 9.32006e+01, atom= 339\n",
      "Step=  936, Dmax= 7.8e-03 nm, Epot= -4.60754e+04 Fmax= 7.53156e+01, atom= 339\n",
      "Step=  937, Dmax= 9.4e-03 nm, Epot= -4.60754e+04 Fmax= 1.28261e+02, atom= 339\n",
      "Step=  938, Dmax= 1.1e-02 nm, Epot= -4.60762e+04 Fmax= 1.16226e+02, atom= 339\n",
      "Step=  940, Dmax= 6.8e-03 nm, Epot= -4.60780e+04 Fmax= 2.95041e+01, atom= 1368\n",
      "Step=  942, Dmax= 4.1e-03 nm, Epot= -4.60788e+04 Fmax= 6.31746e+01, atom= 1368\n",
      "Step=  943, Dmax= 4.9e-03 nm, Epot= -4.60796e+04 Fmax= 4.76729e+01, atom= 1368\n",
      "Step=  944, Dmax= 5.8e-03 nm, Epot= -4.60802e+04 Fmax= 8.41276e+01, atom= 1368\n",
      "Step=  945, Dmax= 7.0e-03 nm, Epot= -4.60810e+04 Fmax= 7.53131e+01, atom= 1368\n",
      "Step=  946, Dmax= 8.4e-03 nm, Epot= -4.60814e+04 Fmax= 1.14408e+02, atom= 1368\n",
      "Step=  947, Dmax= 1.0e-02 nm, Epot= -4.60821e+04 Fmax= 1.15662e+02, atom= 1368\n",
      "Step=  948, Dmax= 1.2e-02 nm, Epot= -4.60822e+04 Fmax= 1.57248e+02, atom= 1368\n",
      "Step=  949, Dmax= 1.5e-02 nm, Epot= -4.60828e+04 Fmax= 1.74987e+02, atom= 1368\n",
      "Step=  951, Dmax= 8.7e-03 nm, Epot= -4.60848e+04 Fmax= 3.01782e+01, atom= 1345\n",
      "Step=  952, Dmax= 1.0e-02 nm, Epot= -4.60855e+04 Fmax= 2.14247e+02, atom= 1368\n",
      "Step=  953, Dmax= 1.3e-02 nm, Epot= -4.60876e+04 Fmax= 8.94970e+01, atom= 1368\n",
      "Step=  955, Dmax= 7.5e-03 nm, Epot= -4.60883e+04 Fmax= 7.76314e+01, atom= 1368\n",
      "Step=  956, Dmax= 9.0e-03 nm, Epot= -4.60887e+04 Fmax= 1.25467e+02, atom= 1368\n",
      "Step=  957, Dmax= 1.1e-02 nm, Epot= -4.60894e+04 Fmax= 1.19966e+02, atom= 1368\n",
      "Step=  959, Dmax= 6.5e-03 nm, Epot= -4.60905e+04 Fmax= 2.95166e+01, atom= 1368\n",
      "Step=  960, Dmax= 7.8e-03 nm, Epot= -4.60914e+04 Fmax= 1.54612e+02, atom= 1368\n",
      "Step=  961, Dmax= 9.4e-03 nm, Epot= -4.60927e+04 Fmax= 6.45018e+01, atom= 1368\n",
      "Step=  963, Dmax= 5.6e-03 nm, Epot= -4.60933e+04 Fmax= 6.11630e+01, atom= 1368\n",
      "Step=  964, Dmax= 6.7e-03 nm, Epot= -4.60939e+04 Fmax= 9.07986e+01, atom= 1368\n",
      "Step=  965, Dmax= 8.1e-03 nm, Epot= -4.60945e+04 Fmax= 9.25017e+01, atom= 1368\n",
      "Step=  966, Dmax= 9.7e-03 nm, Epot= -4.60949e+04 Fmax= 1.26024e+02, atom= 1368\n",
      "Step=  967, Dmax= 1.2e-02 nm, Epot= -4.60954e+04 Fmax= 1.38783e+02, atom= 1368\n",
      "Step=  968, Dmax= 1.4e-02 nm, Epot= -4.60955e+04 Fmax= 1.75522e+02, atom= 1368\n",
      "Step=  969, Dmax= 1.7e-02 nm, Epot= -4.60957e+04 Fmax= 2.07413e+02, atom= 1368\n",
      "Step=  971, Dmax= 1.0e-02 nm, Epot= -4.60980e+04 Fmax= 3.19811e+01, atom= 1345\n",
      "Step=  972, Dmax= 1.2e-02 nm, Epot= -4.60984e+04 Fmax= 2.31645e+02, atom= 1368\n",
      "Step=  973, Dmax= 1.5e-02 nm, Epot= -4.61004e+04 Fmax= 1.20309e+02, atom= 1368\n",
      "Step=  975, Dmax= 8.7e-03 nm, Epot= -4.61013e+04 Fmax= 7.04173e+01, atom= 1368\n",
      "Step=  977, Dmax= 5.2e-03 nm, Epot= -4.61019e+04 Fmax= 4.83563e+01, atom= 1368\n",
      "Step=  978, Dmax= 6.3e-03 nm, Epot= -4.61025e+04 Fmax= 9.28116e+01, atom= 1368\n",
      "Step=  979, Dmax= 7.5e-03 nm, Epot= -4.61032e+04 Fmax= 7.70792e+01, atom= 1368\n",
      "Step=  980, Dmax= 9.0e-03 nm, Epot= -4.61035e+04 Fmax= 1.28397e+02, atom= 1368\n",
      "Step=  981, Dmax= 1.1e-02 nm, Epot= -4.61042e+04 Fmax= 1.15731e+02, atom= 1368\n",
      "Step=  983, Dmax= 6.5e-03 nm, Epot= -4.61052e+04 Fmax= 2.69529e+01, atom= 1368\n",
      "Step=  984, Dmax= 7.8e-03 nm, Epot= -4.61059e+04 Fmax= 1.55765e+02, atom= 1368\n",
      "Step=  985, Dmax= 9.4e-03 nm, Epot= -4.61074e+04 Fmax= 5.79249e+01, atom= 1368\n",
      "Step=  987, Dmax= 5.6e-03 nm, Epot= -4.61079e+04 Fmax= 6.65819e+01, atom= 1368\n",
      "Step=  988, Dmax= 6.7e-03 nm, Epot= -4.61084e+04 Fmax= 8.52191e+01, atom= 1368\n",
      "Step=  989, Dmax= 8.1e-03 nm, Epot= -4.61090e+04 Fmax= 9.58728e+01, atom= 1368\n",
      "Step=  990, Dmax= 9.7e-03 nm, Epot= -4.61093e+04 Fmax= 1.23232e+02, atom= 1368\n",
      "Step=  991, Dmax= 1.2e-02 nm, Epot= -4.61097e+04 Fmax= 1.37459e+02, atom= 1368\n",
      "Step=  992, Dmax= 1.4e-02 nm, Epot= -4.61098e+04 Fmax= 1.79358e+02, atom= 1368\n",
      "Step=  993, Dmax= 1.7e-02 nm, Epot= -4.61099e+04 Fmax= 1.95544e+02, atom= 1368\n",
      "Step=  995, Dmax= 1.0e-02 nm, Epot= -4.61122e+04 Fmax= 2.91625e+01, atom= 1076\n",
      "Step=  996, Dmax= 1.2e-02 nm, Epot= -4.61123e+04 Fmax= 2.26608e+02, atom= 1368\n",
      "Step=  997, Dmax= 1.4e-02 nm, Epot= -4.61145e+04 Fmax= 1.22948e+02, atom= 1368\n",
      "Step=  999, Dmax= 8.7e-03 nm, Epot= -4.61154e+04 Fmax= 6.60313e+01, atom= 1368\n",
      "Step= 1000, Dmax= 1.0e-02 nm, Epot= -4.61151e+04 Fmax= 1.79608e+02, atom= 1368\n",
      "Energy minimization reached the maximum number of steps before the forces\n",
      "reached the requested precision Fmax < 10.\n",
      "\n",
      "writing lowest energy coordinates.\n",
      "\n",
      "Back Off! I just backed up em.pdb to ./#em.pdb.1#\n",
      "\n",
      "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n",
      "Potential Energy  = -4.6115398e+04\n",
      "Maximum force     =  6.6031342e+01 on atom 1368\n",
      "Norm of force     =  3.1664403e+00\n",
      "\n",
      "GROMACS reminds you: \"Everything's formed from particles\" (Van der Graaf Generator)\n",
      "\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top'}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top'}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n",
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Naive you are if you believe life favours those who aren't naive.\" (Piet Hein)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed] All files set up for a run time of 1000 ps (dt=0.01, nsteps=100000)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1087517089\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.132 nm, buffer size 0.032 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.108 nm, buffer size 0.008 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 1 Mb of data\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{'struct': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.gro',\n",
       " 'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top',\n",
       " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx',\n",
       " 'qscript': ['./local.sh'],\n",
       " 'mainselection': None,\n",
       " 'deffnm': 'md',\n",
       " 'includes': ['/home/awsm/MDPOW/mdpow/top',\n",
       "  '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top']}"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from mdpow.equil import WaterSimulation\n",
    "\n",
    "sim = WaterSimulation(\n",
    "    molecule=\"BENZ\",\n",
    "    forcefield=MARTINI,\n",
    "    mdp={\n",
    "        \"energy_minimize\": str(EM_FILE.absolute()),\n",
    "        \"MD_relaxed\": str(EQ_FILE.absolute()),\n",
    "        \"MD_NPT\": str(EQ_FILE.absolute()),\n",
    "        \"MD_restrained\": str(RUN_FILE.absolute()),\n",
    "    },\n",
    "    distance=3.0,\n",
    ")\n",
    "sim.topology(str(BENZENE_ITP))\n",
    "sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n",
    "sim.energy_minimize(maxwarn=1)\n",
    "sim.MD_relaxed(runtime=1e3, dt=0.01)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can execute `mdrun` using `GromacsWrapper`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 10 to 50, rlist from 1.107 to 1.268\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the GPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "100000 steps,   1000.0 ps (continuing from step 100000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 100000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.028        0.007      394.3\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      120.539        0.199\n",
      "\n",
      "GROMACS reminds you: \"I have noticed a large, negative correlation between having a well-defined mission workload and concern for the Top500. It's almost like LINPACK is what you focus on when you don't know what to focus on.\" (Jeff Hammond)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "r = gromacs.run.MDrunner(\n",
    "    dirname=sim.dirs[\"MD_relaxed\"],\n",
    "    deffnm=\"md\",\n",
    "    c=\"md.pdb\",\n",
    "    cpi=True,\n",
    "    v=True,\n",
    ")\n",
    "r.run()  # runs mdrun in the python shell"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now we do the same thing for a longer NPT run, with a longer timestep."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.equil : INFO     Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.gro').\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 't']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt'}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt'}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_relaxed/md.cpt\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n",
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "Last frame         -1 time 1000.000   \n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"This really is a pretty scene, could you ask your kid to smile please?\" (Joe Jackson)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT] All files set up for a run time of 10000 ps (dt=0.02, nsteps=500000)\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1880144435\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.175 nm, buffer size 0.075 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.133 nm, buffer size 0.033 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "Reading Coordinates, Velocities and Box size from old trajectory\n",
      "\n",
      "Will read whole trajectory\n",
      "\n",
      "Using frame at t = 1000 ps\n",
      "\n",
      "Starting time for run is 0 ps\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 10 to 25, rlist from 1.133 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the GPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "500000 steps,  10000.0 ps (continuing from step 500000,  10000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 500000, remaining wall clock time:     0 s          \n",
      "NOTE: 19 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.053        0.013      397.2\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      129.150        0.186\n",
      "\n",
      "GROMACS reminds you: \"This really is a pretty scene, could you ask your kid to smile please?\" (Joe Jackson)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sim.MD(\n",
    "    runtime=1e4, qscript=[\"local.sh\"], dt=0.02\n",
    ")\n",
    "\n",
    "r = gromacs.run.MDrunner(\n",
    "    dirname=sim.dirs[\"MD_NPT\"], deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True\n",
    ")\n",
    "r.run()  # runs mdrun in the python shell"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally, we can set up the thermodynamic integration files. The following will create several directories, one for each $\\lambda$ value:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.fep   : INFO     Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.gro').\n",
      "/home/awsm/MDPOW/mdpow/fep.py:596: UserWarning: Directory 'FEP/water' already exists --- will overwrite existing files.\n",
      "  warnings.warn(wmsg)\n",
      "mdpow.fep   : WARNING  Directory 'FEP/water' already exists --- will overwrite existing files.\n",
      "mdpow.fep   : INFO     Solvation free energy calculation for molecule BENZ in solvent water.\n",
      "mdpow.fep   : INFO     Base directory is '/home/awsm/MDPOW/doc/examples/martini'\n",
      "mdpow.fep   : INFO     Using setup directories under 'FEP/water': {'coulomb': 'FEP/water/Coulomb', 'vdw': 'FEP/water/VDW'}\n",
      "mdpow.fep   : INFO     Default checkpoint file is '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep'\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=0\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n",
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"It's Bicycle Repair Man !\" (Monty Python)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=0.25\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -176167043\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 2 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"And It Goes a Little Something Like This\" (Tag Team)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=0.5\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 1878752383\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 2 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"And It Goes a Little Something Like This\" (Tag Team)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=0.75\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -279132165\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 2 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"The easiest way to scale well is to have bad single-core performance\" (Blind Freddie)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=1\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 970913279\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 2 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"The easiest way to scale well is to have bad single-core performance\" (Blind Freddie)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "gromacs.qsub: WARNING  Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n",
      "mdpow.fep   : INFO     [coulomb] Wrote array job scripts [None]\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -277102597\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 2 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Raw data is like raw sewage, it requires some processing before it can be spread around. The opposite is true of theories.\" (Jim Carr)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.05\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1125393\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Millions saw the apple fall, Newton was the only one who asked why?\" (Bernard Baruch)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.1\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -283645253\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Millions saw the apple fall, Newton was the only one who asked why?\" (Bernard Baruch)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.2\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -33628482\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"I never thought about breaking barriers, I was just interested in what I was doing and kept going.\" (Barbara Liskov)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.3\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 2130180031\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Jesus Not Only Saves, He Also Frequently Makes Backups.\" (Myron Bradshaw)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.4\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 2128084273\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Jesus Not Only Saves, He Also Frequently Makes Backups.\" (Myron Bradshaw)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.5\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1133076737\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.6\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 1543503550\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Numbers have life; they’re not just symbols on paper.\" (Shakuntala Devi)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.65\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1283854372\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"I Was Born to Have Adventure\" (F. Zappa)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.7\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1613856850\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"I Was Born to Have Adventure\" (F. Zappa)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.75\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -335680515\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"The Microsecond is Within Reach\" (P.J. Van Maaren)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.8\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -811074625\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"A protein is a chain of letters.\" (Julie Bernauer)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.85\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -206046313\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"A protein is a chain of letters.\" (Julie Bernauer)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.9\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1214978\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.95\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1481185425\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=1\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -549716569\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 4902.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Sisters Have Always Fascinated Me\" (Speech)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "gromacs.qsub: WARNING  Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n",
      "mdpow.fep   : INFO     [vdw] Wrote array job scripts [None]\n",
      "mdpow.fep   : INFO     Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep'; reload later with G = Ghyd(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/water/Ghyd.fep').\n",
      "mdpow.fep   : INFO     Finished setting up all individual simulations. Now run them...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -136445963\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'W'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.197 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.214 nm, buffer size 0.114 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/top/pp_system.top',\n",
       " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/water/solvation/main.ndx',\n",
       " 'qscript': ['./local.sh'],\n",
       " 'mainselection': None,\n",
       " 'deffnm': 'md',\n",
       " 'includes': ['/home/awsm/MDPOW/mdpow/top'],\n",
       " 'maxwarn': 1,\n",
       " 'couple-intramol': 'no',\n",
       " 'couple_lambda0': 'vdw',\n",
       " 'couple_lambda1': 'none',\n",
       " 'sc_alpha': 0.5,\n",
       " 'sc_power': 1,\n",
       " 'sc_sigma': 0.3,\n",
       " 'separate-dhdl-file': 'no',\n",
       " 'ref_t': 300.0,\n",
       " 'gen_temp': 300.0,\n",
       " 'free_energy': 'yes',\n",
       " 'couple_moltype': 'BENZ',\n",
       " 'init_lambda_state': 15,\n",
       " 'fep_lambdas': array([0.  , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, 0.7 , 0.75,\n",
       "        0.8 , 0.85, 0.9 , 0.95, 1.  ]),\n",
       " 'calc_lambda_neighbors': -1}"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import mdpow.fep\n",
    "\n",
    "gwat = mdpow.fep.Ghyd(simulation=sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n",
    "gwat.setup(dt=0.02)\n",
    "\n",
    "# run multiple simulations on cluster"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "These could be run on a cluster using the `local.sh` scripts, but with Martini they can be done on a local machine in a reasonable amount of time (10-15 minutes on a desktop machine with a GTX 1080). "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.025        0.006      396.8\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      272.359        0.088\n",
      "\n",
      "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.261\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 13 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.049        0.012      398.6\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      139.630        0.172\n",
      "\n",
      "GROMACS reminds you: \"I Caught It In the Face\" (P.J. Harvey)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 15 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.168        0.042      398.1\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       40.992        0.585\n",
      "\n",
      "GROMACS reminds you: \"I was a bit of an artist, and somewhere along the way had gotten the idea that computers could be used for animation and artists, because in-betweening was so tedious... Of course, everyone thought I was nuts.\" (Carla Meninsky, Atari engineer)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 20 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.031        0.008      397.9\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      218.840        0.110\n",
      "\n",
      "GROMACS reminds you: \"Here's the Way It Might End\" (G. Michael)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.025        0.006      397.2\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      275.308        0.087\n",
      "\n",
      "GROMACS reminds you: \"Christianity may be OK between consenting adults in private but should not be taught to young children.\" (Francis Crick)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.031        0.008      397.4\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      224.333        0.107\n",
      "\n",
      "GROMACS reminds you: \"Move about like a Scientist, lay down, get kissed\" (Red Hot Chili Peppars)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.261\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 26 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.035        0.009      397.9\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      195.832        0.123\n",
      "\n",
      "GROMACS reminds you: \"Move about like a Scientist, lay down, get kissed\" (Red Hot Chili Peppars)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.047        0.012      398.2\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      146.089        0.164\n",
      "\n",
      "GROMACS reminds you: \"Restraint! What possible restraint?\" (Joseph Conrad)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.030        0.008      397.4\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      225.401        0.106\n",
      "\n",
      "GROMACS reminds you: \"I'm a Jerk\" (F. Black)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 15 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.029        0.007      397.2\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      237.803        0.101\n",
      "\n",
      "GROMACS reminds you: \"Two chemists walk into a bar. The first one says, 'I'll have some H2O.'. The second one says, 'I'll have some H2O, too'. He dies.\" (Anonymous)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 24 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.056        0.014      398.6\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      121.934        0.197\n",
      "\n",
      "GROMACS reminds you: \"Two chemists walk into a bar. The first one says, 'I'll have some H2O.'. The second one says, 'I'll have some H2O, too'. He dies.\" (Anonymous)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 30 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.047        0.012      398.3\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      145.534        0.165\n",
      "\n",
      "GROMACS reminds you: \"Shake Yourself\" (YES)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 12 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.024        0.006      396.8\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      291.637        0.082\n",
      "\n",
      "GROMACS reminds you: \"I think everybody should like everybody.\" (Andy Warhol)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 26 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.044        0.011      398.4\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      155.175        0.155\n",
      "\n",
      "GROMACS reminds you: \"Shit Happens\" (Pulp Fiction)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.034        0.009      397.6\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      203.183        0.118\n",
      "\n",
      "GROMACS reminds you: \"A curious aspect of the theory of evolution is that everybody thinks he understands it.\" (Jacques Monod)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 17 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.023        0.006      396.7\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      303.368        0.079\n",
      "\n",
      "GROMACS reminds you: \"If it weren't for bad luck, we'd have no luck at all\" (The Unthanks)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 36 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.045        0.011      398.3\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      152.222        0.158\n",
      "\n",
      "GROMACS reminds you: \"If it weren't for bad luck, we'd have no luck at all\" (The Unthanks)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 11 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.029        0.007      397.4\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      233.731        0.103\n",
      "\n",
      "GROMACS reminds you: \"Move Over Hogey Bear\" (Urban Dance Squad)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.214 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 12 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.029        0.007      397.6\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      233.889        0.103\n",
      "\n",
      "GROMACS reminds you: \"Scientists do not join hands every Sunday and sing \"Yes gravity is real! I know gravity is real! I will have faith! I believe in my heart that what goes up, up, up must come down, down, down. Amen!\" If they did, we would think they were pretty insecure about the concept.\" (Dan Barker)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 15 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.024        0.006      396.9\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      283.481        0.085\n",
      "\n",
      "GROMACS reminds you: \"Scientists do not join hands every Sunday and sing \"Yes gravity is real! I know gravity is real! I will have faith! I believe in my heart that what goes up, up, up must come down, down, down. Amen!\" If they did, we would think they were pretty insecure about the concept.\" (Dan Barker)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.215 to 1.262\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.028        0.007      397.4\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      242.660        0.099\n",
      "\n",
      "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n"
     ]
    }
   ],
   "source": [
    "for dir_ in gwat.fep_dirs():\n",
    "    r = gromacs.run.MDrunner(\n",
    "        dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=True\n",
    "    )\n",
    "    r.run()  # runs mdrun in the python shell"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally, we read the `.edr` files from the disk to get the energy reported by Gromacs and use `alchemlyb` to determine the free energy of solvation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.fep   : INFO     [FEP/water] Converting EDR -> XVG.bz2\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg\n",
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg\n",
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg\n",
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/#md.xvg.1#\n",
      "Reading energy frame    140 time  560.000         mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"I always seem to get inspiration and renewed vitality by contact with this great novel land of yours which sticks up out of the Atlantic.\" (Winston Churchill)\n",
      "\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/#md.xvg.1#\n",
      "Reading energy frame     13 time   52.000         "
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/#md.xvg.1#\n",
      "Reading energy frame    200 time  800.000         mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n",
      "Last energy frame read 250 time 1000.000         \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/#md.xvg.1#\n",
      "Reading energy frame    200 time  800.000         mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n",
      "Last energy frame read 250 time 1000.000         \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Computers are like humans - they do everything except think.\" (John von Neumann)\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"set: No match.\" (tcsh)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame      0 time    0.000         \n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/#md.xvg.1#\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"set: No match.\" (tcsh)\n",
      "\n",
      "mdpow.fep   : INFO     Analysis stride is 1.\n",
      "mdpow.fep   : INFO     Analysis starts from frame 0.\n",
      "mdpow.fep   : INFO     Analysis stops at frame None.\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg' with bzip2\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0000/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0250/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0500/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/0750/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/Coulomb/1000/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0000/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0050/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0100/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0200/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0300/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0400/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0500/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0600/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0650/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0700/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0750/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0800/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0850/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0900/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/0950/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/water] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/water/VDW/1000/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/water] Finding dgdl xvg files, reading with stride=1 permissive=False.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 0000\n",
      "\u001b[32m2023-09-04 22:40:31.863\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:31.865\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.78.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:31.866\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 12.9740.\n",
      "mdpow.fep   : INFO     The data are subsampled every 13 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 0250\n",
      "\u001b[32m2023-09-04 22:40:31.949\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:31.951\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 20.06.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:31.952\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 238.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 10.4664.\n",
      "mdpow.fep   : INFO     The data are subsampled every 11 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 0500\n",
      "\u001b[32m2023-09-04 22:40:32.022\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.028\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 43.47.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.030\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 114.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 21.8509.\n",
      "mdpow.fep   : INFO     The data are subsampled every 22 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 0750\n",
      "\u001b[32m2023-09-04 22:40:32.108\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.109\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 23.00.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.111\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 208.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 11.9760.\n",
      "mdpow.fep   : INFO     The data are subsampled every 12 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 1000\n",
      "\u001b[32m2023-09-04 22:40:32.180\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.182\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 33.72.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.184\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 147.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 16.9456.\n",
      "mdpow.fep   : INFO     The data are subsampled every 17 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0000\n",
      "\u001b[32m2023-09-04 22:40:32.400\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.402\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 34.54.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.403\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 143.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 17.4196.\n",
      "mdpow.fep   : INFO     The data are subsampled every 18 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0050\n",
      "\u001b[32m2023-09-04 22:40:32.612\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.615\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 20.10.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.616\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 238.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 10.4664.\n",
      "mdpow.fep   : INFO     The data are subsampled every 11 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0100\n",
      "\u001b[32m2023-09-04 22:40:32.824\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.825\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.47.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:32.826\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 11.4793.\n",
      "mdpow.fep   : INFO     The data are subsampled every 12 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0200\n",
      "\u001b[32m2023-09-04 22:40:33.054\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:33.056\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 27.85.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:33.057\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 178.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 13.9944.\n",
      "mdpow.fep   : INFO     The data are subsampled every 14 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0300\n",
      "\u001b[32m2023-09-04 22:40:33.298\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:33.300\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 27.51.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:33.302\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 178.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 13.9944.\n",
      "mdpow.fep   : INFO     The data are subsampled every 14 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0400\n",
      "\u001b[32m2023-09-04 22:40:33.555\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:33.557\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.25.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:33.558\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 12.9740.\n",
      "mdpow.fep   : INFO     The data are subsampled every 13 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0500\n",
      "\u001b[32m2023-09-04 22:40:33.818\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:33.820\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 24.63.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:33.820\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 200.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 12.4550.\n",
      "mdpow.fep   : INFO     The data are subsampled every 13 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0600\n",
      "\u001b[32m2023-09-04 22:40:34.042\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:34.047\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 42.95.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:34.048\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 116.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 21.4741.\n",
      "mdpow.fep   : INFO     The data are subsampled every 22 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0650\n",
      "\u001b[32m2023-09-04 22:40:34.274\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:34.276\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.73.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:34.277\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 11.4793.\n",
      "mdpow.fep   : INFO     The data are subsampled every 12 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0700\n",
      "\u001b[32m2023-09-04 22:40:34.611\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:34.616\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.96.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:34.617\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 11.4793.\n",
      "mdpow.fep   : INFO     The data are subsampled every 12 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0750\n",
      "\u001b[32m2023-09-04 22:40:34.863\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:34.865\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.68.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:34.866\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 12.9740.\n",
      "mdpow.fep   : INFO     The data are subsampled every 13 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0800\n",
      "\u001b[32m2023-09-04 22:40:35.091\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.094\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 32.94.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.095\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 151.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 16.4967.\n",
      "mdpow.fep   : INFO     The data are subsampled every 17 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0850\n",
      "\u001b[32m2023-09-04 22:40:35.343\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.349\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 40.21.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.350\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 122.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 20.4180.\n",
      "mdpow.fep   : INFO     The data are subsampled every 21 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0900\n",
      "\u001b[32m2023-09-04 22:40:35.564\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.567\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 29.12.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.568\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 167.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 14.9162.\n",
      "mdpow.fep   : INFO     The data are subsampled every 15 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0950\n",
      "\u001b[32m2023-09-04 22:40:35.787\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.788\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.51.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.789\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 9.4715.\n",
      "mdpow.fep   : INFO     The data are subsampled every 10 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 1000\n",
      "\u001b[32m2023-09-04 22:40:35.996\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.998\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 22.19.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:40:35.999\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 217.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 11.4793.\n",
      "mdpow.fep   : INFO     The data are subsampled every 12 frames.\n",
      "mdpow.fep   : INFO     DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n",
      "mdpow.fep   : INFO     [BENZ] Water solvation free energy (coulomb) 1.10771e-15 (0.00) kJ/mol\n",
      "mdpow.fep   : INFO     [BENZ] Water solvation free energy (vdw) -6.74471 (0.27) kJ/mol\n",
      "mdpow.fep   : INFO     [BENZ] Water solvation free energy (Gibbs) 6.74471 (0.27) kJ/mol\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "6.74471 (0.269555)"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gwat.convert_edr()\n",
    "gwat.analyze_alchemlyb()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Octanol solvation\n",
    "\n",
    "Now, we repeat the exact same steps as above but using an `OctanolSimulation`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.equil : INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top] Created topology 'system.top' that includes 'martini_v3.0.0_small_molecules_v1.itp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] Solvating with water '/home/awsm/MDPOW/doc/examples/martini/octanol.gro'...\n",
      "                     :-) GROMACS - gmx editconf, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n",
      "Command line:\n",
      "  gmx editconf -f /home/awsm/MDPOW/doc/examples/martini/benzene.pdb -o boxed.gro -bt dodecahedron -d 4.0\n",
      "\n",
      "\n",
      "Back Off! I just backed up boxed.gro to ./#boxed.gro.1#\n",
      "\n",
      "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n",
      "\n",
      "                     :-) GROMACS - gmx solvate, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n",
      "Command line:\n",
      "  gmx solvate -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -cp boxed.gro -cs /home/awsm/MDPOW/doc/examples/martini/octanol.gro -o solvated.gro\n",
      "\n",
      "Reading solute configuration\n",
      "Reading solvent configuration\n",
      "\n",
      "Initialising inter-atomic distances...\n",
      "Generating solvent configuration\n",
      "Will generate new solvent configuration of 2x2x2 boxes\n",
      "Solvent box contains 5943 atoms in 1981 residues\n",
      "Removed 828 solvent atoms due to solvent-solvent overlap\n",
      "Removed 3 solvent atoms due to solute-solvent overlap\n",
      "Sorting configuration\n",
      "Found 1 molecule type:\n",
      "    OCO (   3 atoms):  1704 residues\n",
      "Generated solvent containing 5112 atoms in 1704 residues\n",
      "Writing generated configuration to solvated.gro\n",
      "\n",
      "Back Off! I just backed up solvated.gro to ./#solvated.gro.1#\n",
      "\n",
      "Output configuration contains 5115 atoms in 1705 residues\n",
      "Volume                 :     399.981 (nm^3)\n",
      "Density                :     389.199 (g/l)\n",
      "Number of solvent molecules:   1704   \n",
      "\n",
      "Processing topology\n",
      "\n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#system.top.2#\n",
      "\n",
      "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n",
      "\n",
      "gromacs.setup: INFO     Solvated system with /home/awsm/MDPOW/doc/examples/martini/octanol.gro\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Note that major changes are planned in future for editconf, to improve usability and utility.\n",
      "Read 3 atoms\n",
      "Volume: 4050 nm^3, corresponds to roughly 1822500 electrons\n",
      "No velocities found\n",
      "    system size :  0.210  0.160  0.248 (nm)\n",
      "    diameter    :  0.270               (nm)\n",
      "    center      :  2.987  0.606  2.315 (nm)\n",
      "    box vectors : 15.000 15.000 18.000 (nm)\n",
      "    box angles  :  90.00  90.00  90.00 (degrees)\n",
      "    box volume  :4050.00               (nm^3)\n",
      "    shift       :  3.216  5.597  0.609 (nm)\n",
      "new center      :  6.203  6.203  2.924 (nm)\n",
      "new box vectors :  8.270  8.270  8.270 (nm)\n",
      "new box angles  :  60.00  60.00  90.00 (degrees)\n",
      "new box volume  : 399.98               (nm^3)\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary. Note, that this functionality may\n",
      "         be removed in a future GROMACS version. Please, consider\n",
      "         using another file format for your input.\n",
      "\n",
      "NOTE: From version 5.0 gmx solvate uses the Van der Waals radii\n",
      "from the source below. This means the results may be different\n",
      "compared to previous GROMACS versions.\n",
      "\n",
      "++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n",
      "A. Bondi\n",
      "van der Waals Volumes and Radii\n",
      "J. Phys. Chem. 68 (1964) pp. 441-451\n",
      "-------- -------- --- Thank You --- -------- --------\n",
      "\n",
      "Adding line for 1704 solvent molecules with resname (OCO) to topology file (/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "gromacs.cbook: INFO     system total charge qtot = 0\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation] After solvation: total charge qtot = 0 = 0\n",
      "gromacs.cbook: INFO     system total charge qtot = 0\n",
      "gromacs.setup: INFO     Building the main index file 'main.ndx'...\n",
      "                     :-) GROMACS - gmx make_ndx, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n",
      "Command line:\n",
      "  gmx make_ndx -f ionized.tpr -o main.ndx\n",
      "\n",
      "\n",
      "Reading structure file\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "\n",
      "Back Off! I just backed up main.ndx to ./#main.ndx.2#\n",
      "\n",
      "GROMACS reminds you: \"Sir, spare your threats: The bug which you would fright me with I seek.\" (Hermione, Act III, scene II of Shakespeare's Winter's Tale)\n",
      "\n",
      "                     :-) GROMACS - gmx make_ndx, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n",
      "Command line:\n",
      "  gmx make_ndx -f ionized.tpr -n main.ndx -o main.ndx\n",
      "\n",
      "\n",
      "Reading structure file\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "\n",
      "Back Off! I just backed up main.ndx to ./#main.ndx.3#\n",
      "\n",
      "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n",
      "\n",
      "                     :-) GROMACS - gmx trjconv, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation\n",
      "Command line:\n",
      "  gmx trjconv -ur compact -center -boxcenter tric -pbc mol -f ionized.gro -s ionized.tpr -o compact.pdb -n main.ndx\n",
      "\n",
      "Will write pdb: Protein data bank file\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "Reading file ionized.tpr, VERSION 2023.2 (single precision)\n",
      "Group     0 (         System) has  5115 elements\n",
      "Group     1 (          Other) has  5115 elements\n",
      "Group     2 (           BENZ) has     3 elements\n",
      "Group     3 (            OCO) has  5112 elements\n",
      "Group     4 (       __main__) has     3 elements\n",
      "Group     5 (__environment__) has  5112 elements\n",
      "Select a group: Group     0 (         System) has  5115 elements\n",
      "Group     1 (          Other) has  5115 elements\n",
      "Group     2 (           BENZ) has     3 elements\n",
      "Group     3 (            OCO) has  5112 elements\n",
      "Group     4 (       __main__) has     3 elements\n",
      "Group     5 (__environment__) has  5112 elements\n",
      "Select a group: Reading frames from gro file 'This is an auto generated system', 5115 atoms.\n",
      "Reading frame       0 time    0.000   \n",
      "Precision of ionized.gro is 0.001 (nm)\n",
      "\n",
      "Back Off! I just backed up compact.pdb to ./#compact.pdb.1#\n",
      "Last frame          0 time    0.000   \n",
      " ->  frame      0 time    0.000      \n",
      "Last written: frame      0 time    0.000\n",
      "\n",
      "\n",
      "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n",
      "\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx grompp -maxwarn 1 -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -pp /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -f /tmp/tmpxe8vdy7l.mdp -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -nov\n",
      "\n",
      "\n",
      "NOTE 1 [file /tmp/tmpxe8vdy7l.mdp]:\n",
      "  For a correct single-point energy evaluation with nsteps = 0, use\n",
      "  continuation = yes to avoid constraining the input coordinates.\n",
      "\n",
      "\n",
      "Back Off! I just backed up /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top to /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/#pp_system.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Note that major changes are planned in future for trjconv, to improve usability and utility.\n",
      "Select group for centering\n",
      "Selected 4: '__main__'\n",
      "Select group for output\n",
      "Selected 0: 'System'\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "NOTE 2 [file system.top, line 28]:\n",
      "  For energy conservation with LINCS, lincs_iter should be 2 or larger.\n",
      "\n",
      "\n",
      "Number of degrees of freedom in T-Coupling group rest is 15339.00\n",
      "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n",
      "\n",
      "NOTE 3 [file /tmp/tmpxe8vdy7l.mdp]:\n",
      "  NVE simulation with an initial temperature of zero: will use a Verlet\n",
      "  buffer of 10%. Check your energy drift!\n",
      "\n",
      "\n",
      "There were 3 NOTEs\n",
      "\n",
      "GROMACS reminds you: \"The physical chemists never use their eyes and are most lamentably lacking in chemical culture. It is essential to cast out from our midst, root and branch, this physical element and return to our laboratories.\" (Henry Edward Armstrong)\n",
      "\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] Energy minimization of struct='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro', top='/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top', mdp='em.mdp' ...\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/em.mdp': dict_keys(['maxwarn', 'pp', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'em.mdp': ['maxwarn', 'pp']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'maxwarn': 1, 'pp': 'processed.top'}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'maxwarn': 1, 'pp': 'processed.top'}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n",
      "Command line:\n",
      "  gmx grompp -f em.mdp -o em.tpr -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -r /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/solvated.gro -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -maxwarn 1 -pp processed.top\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -105579659\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "Analysing residue names:\n",
      "There are:  1705      Other residues\n",
      "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
      "\n",
      "This run will generate roughly 0 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group rest is 15339.00\n",
      "The integrator does not provide a ensemble temperature, there is no system ensemble temperature\n",
      "\n",
      "Back Off! I just backed up em.tpr to ./#em.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"You Can Always Go On Ricky Lake\" (Offspring)\n",
      "\n",
      "gromacs.run : WARNING  No 'mdrun_d' binary found so trying 'mdrun' instead.\n",
      "(Note that energy minimization runs better with mdrun_d.)\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/run.py:423: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead.\n",
      "(Note that energy minimization runs better with mdrun_d.)\n",
      "  warnings.warn(wmsg, category=AutoCorrectionWarning)\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em\n",
      "Command line:\n",
      "  gmx mdrun -v -stepout 10 -deffnm em -c em.pdb\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 1459009023\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "Analysing residue names:\n",
      "There are:  1705      Other residues\n",
      "Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n",
      "\n",
      "This run will generate roughly 1 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "Back Off! I just backed up em.log to ./#em.log.1#\n",
      "Reading file em.tpr, VERSION 2023.2 (single precision)\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "\n",
      "Back Off! I just backed up em.trr to ./#em.trr.1#\n",
      "\n",
      "Back Off! I just backed up em.edr to ./#em.edr.1#\n",
      "\n",
      "Steepest Descents:\n",
      "   Tolerance (Fmax)   =  1.00000e+01\n",
      "   Number of steps    =         1000\n",
      "Step=    0, Dmax= 1.0e-02 nm, Epot=  1.02801e+07 Fmax= 2.05315e+07, atom= 5083\n",
      "Step=    1, Dmax= 1.0e-02 nm, Epot=  7.41994e+06 Fmax= 5.74654e+06, atom= 3110\n",
      "Step=    2, Dmax= 1.2e-02 nm, Epot=  4.40326e+06 Fmax= 2.44532e+06, atom= 4997\n",
      "Step=    3, Dmax= 1.4e-02 nm, Epot=  2.73795e+06 Fmax= 9.51879e+05, atom= 1685\n",
      "Step=    4, Dmax= 1.7e-02 nm, Epot=  1.53428e+06 Fmax= 4.51665e+05, atom= 1684\n",
      "Step=    5, Dmax= 2.1e-02 nm, Epot=  8.87445e+05 Fmax= 1.90248e+05, atom= 1990\n",
      "Step=    6, Dmax= 2.5e-02 nm, Epot=  4.61156e+05 Fmax= 1.05731e+05, atom= 3691\n",
      "Step=    7, Dmax= 3.0e-02 nm, Epot=  2.59013e+05 Fmax= 7.39295e+04, atom= 3626\n",
      "Step=    8, Dmax= 3.6e-02 nm, Epot=  1.57144e+05 Fmax= 4.51091e+04, atom= 3691\n",
      "Step=    9, Dmax= 4.3e-02 nm, Epot=  8.70638e+04 Fmax= 3.11807e+04, atom= 3047\n",
      "Step=   10, Dmax= 5.2e-02 nm, Epot=  4.74060e+04 Fmax= 1.09883e+05, atom= 3020\n",
      "Step=   11, Dmax= 6.2e-02 nm, Epot=  3.89493e+04 Fmax= 1.54250e+04, atom= 1088\n",
      "Step=   12, Dmax= 7.4e-02 nm, Epot=  6.83725e+03 Fmax= 1.68745e+04, atom= 1088\n",
      "Step=   13, Dmax= 8.9e-02 nm, Epot= -4.12860e+03 Fmax= 1.03436e+04, atom= 1088\n",
      "Step=   14, Dmax= 1.1e-01 nm, Epot= -1.13031e+04 Fmax= 1.60202e+05, atom= 4\n",
      "Step=   15, Dmax= 1.3e-01 nm, Epot= -1.48685e+04 Fmax= 1.22373e+04, atom= 4\n",
      "Step=   16, Dmax= 1.5e-01 nm, Epot= -2.01121e+04 Fmax= 3.01368e+04, atom= 4\n",
      "Step=   17, Dmax= 1.8e-01 nm, Epot= -2.17951e+04 Fmax= 4.10915e+04, atom= 2520\n",
      "Step=   18, Dmax= 2.2e-01 nm, Epot= -2.41457e+04 Fmax= 2.58494e+04, atom= 4\n",
      "Step=   19, Dmax= 2.7e-01 nm, Epot= -2.66241e+04 Fmax= 2.69426e+04, atom= 835\n",
      "Step=   23, Dmax= 4.0e-02 nm, Epot= -2.72906e+04 Fmax= 1.12460e+04, atom= 5360\n",
      "Step=   24, Dmax= 4.8e-02 nm, Epot= -2.82619e+04 Fmax= 8.89296e+03, atom= 3110\n",
      "Step=   25, Dmax= 5.8e-02 nm, Epot= -2.94485e+04 Fmax= 7.02511e+03, atom= 835\n",
      "Step=   26, Dmax= 6.9e-02 nm, Epot= -3.10719e+04 Fmax= 4.20729e+03, atom= 835\n",
      "Step=   27, Dmax= 8.3e-02 nm, Epot= -3.33641e+04 Fmax= 1.18154e+04, atom= 835\n",
      "Step=   28, Dmax= 9.9e-02 nm, Epot= -3.46020e+04 Fmax= 2.13219e+03, atom= 3110\n",
      "Step=   29, Dmax= 1.2e-01 nm, Epot= -3.82089e+04 Fmax= 4.27789e+04, atom= 3110\n",
      "Step=   30, Dmax= 1.4e-01 nm, Epot= -3.94414e+04 Fmax= 2.82683e+03, atom= 536\n",
      "Step=   31, Dmax= 1.7e-01 nm, Epot= -3.96515e+04 Fmax= 1.23669e+05, atom= 413\n",
      "Step=   33, Dmax= 1.0e-01 nm, Epot= -4.13623e+04 Fmax= 3.78120e+04, atom= 413\n",
      "Step=   34, Dmax= 1.2e-01 nm, Epot= -4.20929e+04 Fmax= 3.45758e+03, atom= 5051\n",
      "Step=   35, Dmax= 1.5e-01 nm, Epot= -4.35947e+04 Fmax= 9.20874e+03, atom= 5051\n",
      "Step=   36, Dmax= 1.8e-01 nm, Epot= -4.39134e+04 Fmax= 4.39989e+03, atom= 413\n",
      "Step=   37, Dmax= 2.1e-01 nm, Epot= -4.44859e+04 Fmax= 2.43471e+04, atom= 5050\n",
      "Step=   39, Dmax= 1.3e-01 nm, Epot= -4.46805e+04 Fmax= 3.27215e+04, atom= 5113\n",
      "Step=   40, Dmax= 1.5e-01 nm, Epot= -4.53859e+04 Fmax= 6.23654e+03, atom= 1883\n",
      "Step=   42, Dmax= 9.2e-02 nm, Epot= -4.59237e+04 Fmax= 1.73940e+03, atom= 1883\n",
      "Step=   43, Dmax= 1.1e-01 nm, Epot= -4.70801e+04 Fmax= 2.89875e+03, atom= 1883\n",
      "Step=   44, Dmax= 1.3e-01 nm, Epot= -4.77589e+04 Fmax= 3.05609e+03, atom= 1360\n",
      "Step=   45, Dmax= 1.6e-01 nm, Epot= -4.80474e+04 Fmax= 1.33101e+04, atom= 1360\n",
      "Step=   46, Dmax= 1.9e-01 nm, Epot= -4.84228e+04 Fmax= 6.33088e+03, atom= 567\n",
      "Step=   48, Dmax= 1.1e-01 nm, Epot= -4.88170e+04 Fmax= 1.25395e+03, atom= 1608\n",
      "Step=   49, Dmax= 1.4e-01 nm, Epot= -4.97575e+04 Fmax= 4.33496e+03, atom= 693\n",
      "Step=   50, Dmax= 1.7e-01 nm, Epot= -5.01312e+04 Fmax= 3.75784e+03, atom= 1338\n",
      "Step=   52, Dmax= 9.9e-02 nm, Epot= -5.02226e+04 Fmax= 9.33880e+03, atom= 2954\n",
      "Step=   54, Dmax= 6.0e-02 nm, Epot= -5.04442e+04 Fmax= 1.97341e+03, atom= 144\n",
      "Step=   55, Dmax= 7.1e-02 nm, Epot= -5.07143e+04 Fmax= 1.32154e+03, atom= 144\n",
      "Step=   56, Dmax= 8.6e-02 nm, Epot= -5.11246e+04 Fmax= 1.28381e+03, atom= 144\n",
      "Step=   57, Dmax= 1.0e-01 nm, Epot= -5.15390e+04 Fmax= 2.41925e+03, atom= 144\n",
      "Step=   58, Dmax= 1.2e-01 nm, Epot= -5.18157e+04 Fmax= 1.10336e+03, atom= 2954\n",
      "Step=   60, Dmax= 7.4e-02 nm, Epot= -5.21376e+04 Fmax= 1.22571e+03, atom= 3046\n",
      "Step=   62, Dmax= 4.4e-02 nm, Epot= -5.22802e+04 Fmax= 1.99710e+03, atom= 3046\n",
      "Step=   63, Dmax= 5.3e-02 nm, Epot= -5.24430e+04 Fmax= 1.13368e+03, atom= 444\n",
      "Step=   64, Dmax= 6.4e-02 nm, Epot= -5.26101e+04 Fmax= 2.51858e+03, atom= 444\n",
      "Step=   65, Dmax= 7.7e-02 nm, Epot= -5.27376e+04 Fmax= 1.69816e+03, atom= 3046\n",
      "Step=   66, Dmax= 9.2e-02 nm, Epot= -5.27505e+04 Fmax= 4.60827e+03, atom= 3046\n",
      "Step=   67, Dmax= 1.1e-01 nm, Epot= -5.29464e+04 Fmax= 2.66046e+03, atom= 444\n",
      "Step=   68, Dmax= 1.3e-01 nm, Epot= -5.30886e+04 Fmax= 3.10115e+03, atom= 1079\n",
      "Step=   70, Dmax= 8.0e-02 nm, Epot= -5.32855e+04 Fmax= 8.36880e+02, atom= 1079\n",
      "Step=   72, Dmax= 4.8e-02 nm, Epot= -5.34753e+04 Fmax= 1.52218e+03, atom= 2567\n",
      "Step=   73, Dmax= 5.7e-02 nm, Epot= -5.35846e+04 Fmax= 9.08475e+02, atom= 3179\n",
      "Step=   74, Dmax= 6.9e-02 nm, Epot= -5.37531e+04 Fmax= 3.31739e+03, atom= 2567\n",
      "Step=   75, Dmax= 8.3e-02 nm, Epot= -5.38422e+04 Fmax= 8.90771e+02, atom= 3179\n",
      "Step=   76, Dmax= 9.9e-02 nm, Epot= -5.39374e+04 Fmax= 7.71798e+03, atom= 2567\n",
      "Step=   77, Dmax= 1.2e-01 nm, Epot= -5.41298e+04 Fmax= 1.05874e+03, atom= 2567\n",
      "Step=   79, Dmax= 7.1e-02 nm, Epot= -5.43156e+04 Fmax= 5.14630e+02, atom= 4622\n",
      "Step=   80, Dmax= 8.6e-02 nm, Epot= -5.43995e+04 Fmax= 1.02555e+04, atom= 4622\n",
      "Step=   81, Dmax= 1.0e-01 nm, Epot= -5.46246e+04 Fmax= 1.13109e+03, atom= 3179\n",
      "Step=   82, Dmax= 1.2e-01 nm, Epot= -5.48060e+04 Fmax= 1.37699e+03, atom= 2567\n",
      "Step=   83, Dmax= 1.5e-01 nm, Epot= -5.48334e+04 Fmax= 2.05696e+03, atom= 2567\n",
      "Step=   84, Dmax= 1.8e-01 nm, Epot= -5.49886e+04 Fmax= 2.14840e+03, atom= 2567\n",
      "Step=   85, Dmax= 2.1e-01 nm, Epot= -5.50857e+04 Fmax= 2.05082e+03, atom= 2567\n",
      "Step=   87, Dmax= 1.3e-01 nm, Epot= -5.52320e+04 Fmax= 9.84210e+02, atom= 2567\n",
      "Step=   89, Dmax= 7.7e-02 nm, Epot= -5.54016e+04 Fmax= 7.76042e+02, atom= 4623\n",
      "Step=   90, Dmax= 9.2e-02 nm, Epot= -5.54718e+04 Fmax= 2.97639e+03, atom= 3180\n",
      "Step=   91, Dmax= 1.1e-01 nm, Epot= -5.55854e+04 Fmax= 7.51557e+02, atom= 3180\n",
      "Step=   93, Dmax= 6.6e-02 nm, Epot= -5.57277e+04 Fmax= 5.56224e+02, atom= 2566\n",
      "Step=   94, Dmax= 7.9e-02 nm, Epot= -5.58208e+04 Fmax= 8.09355e+02, atom= 3568\n",
      "Step=   95, Dmax= 9.5e-02 nm, Epot= -5.58278e+04 Fmax= 3.70043e+03, atom= 3015\n",
      "Step=   96, Dmax= 1.1e-01 nm, Epot= -5.59803e+04 Fmax= 7.92915e+02, atom= 3015\n",
      "Step=   97, Dmax= 1.4e-01 nm, Epot= -5.60522e+04 Fmax= 1.74485e+03, atom= 3528\n",
      "Step=   99, Dmax= 8.2e-02 nm, Epot= -5.61793e+04 Fmax= 1.30159e+03, atom= 3207\n",
      "Step=  100, Dmax= 9.9e-02 nm, Epot= -5.62395e+04 Fmax= 1.73043e+03, atom= 3306\n",
      "Step=  101, Dmax= 1.2e-01 nm, Epot= -5.63205e+04 Fmax= 3.38021e+02, atom= 2922\n",
      "Step=  102, Dmax= 1.4e-01 nm, Epot= -5.63321e+04 Fmax= 3.14597e+03, atom= 3306\n",
      "Step=  103, Dmax= 1.7e-01 nm, Epot= -5.66195e+04 Fmax= 9.63577e+02, atom= 3306\n",
      "Step=  105, Dmax= 1.0e-01 nm, Epot= -5.66649e+04 Fmax= 2.46338e+03, atom= 3207\n",
      "Step=  106, Dmax= 1.2e-01 nm, Epot= -5.66681e+04 Fmax= 2.93470e+03, atom= 3528\n",
      "Step=  107, Dmax= 1.5e-01 nm, Epot= -5.67116e+04 Fmax= 9.98182e+02, atom= 3015\n",
      "Step=  108, Dmax= 1.8e-01 nm, Epot= -5.67160e+04 Fmax= 4.01710e+03, atom= 3568\n",
      "Step=  109, Dmax= 2.1e-01 nm, Epot= -5.67314e+04 Fmax= 2.60014e+03, atom= 4623\n",
      "Step=  110, Dmax= 2.6e-01 nm, Epot= -5.68128e+04 Fmax= 1.55369e+03, atom= 4632\n",
      "Step=  112, Dmax= 1.5e-01 nm, Epot= -5.69097e+04 Fmax= 9.06986e+02, atom= 4624\n",
      "Step=  114, Dmax= 9.2e-02 nm, Epot= -5.70090e+04 Fmax= 5.23911e+02, atom= 4624\n",
      "Step=  116, Dmax= 5.5e-02 nm, Epot= -5.70881e+04 Fmax= 4.07709e+02, atom= 4625\n",
      "Step=  117, Dmax= 6.6e-02 nm, Epot= -5.71193e+04 Fmax= 7.37738e+02, atom= 4625\n",
      "Step=  118, Dmax= 7.9e-02 nm, Epot= -5.71803e+04 Fmax= 7.59541e+02, atom= 4625\n",
      "Step=  119, Dmax= 9.5e-02 nm, Epot= -5.72119e+04 Fmax= 8.99682e+02, atom= 4625\n",
      "Step=  121, Dmax= 5.7e-02 nm, Epot= -5.73265e+04 Fmax= 2.51483e+02, atom= 2558\n",
      "Step=  123, Dmax= 3.4e-02 nm, Epot= -5.73747e+04 Fmax= 4.44440e+02, atom= 2558\n",
      "Step=  124, Dmax= 4.1e-02 nm, Epot= -5.74121e+04 Fmax= 3.55337e+02, atom= 4635\n",
      "Step=  125, Dmax= 4.9e-02 nm, Epot= -5.74287e+04 Fmax= 1.20535e+03, atom= 285\n",
      "Step=  126, Dmax= 5.9e-02 nm, Epot= -5.74910e+04 Fmax= 3.55226e+02, atom= 285\n",
      "Step=  127, Dmax= 7.1e-02 nm, Epot= -5.75302e+04 Fmax= 1.48864e+03, atom= 285\n",
      "Step=  128, Dmax= 8.5e-02 nm, Epot= -5.75701e+04 Fmax= 6.22858e+02, atom= 4635\n",
      "Step=  130, Dmax= 5.1e-02 nm, Epot= -5.76114e+04 Fmax= 3.83218e+02, atom= 5043\n",
      "Step=  131, Dmax= 6.1e-02 nm, Epot= -5.76603e+04 Fmax= 4.35957e+02, atom= 5043\n",
      "Step=  133, Dmax= 3.7e-02 nm, Epot= -5.76969e+04 Fmax= 3.00286e+02, atom= 4635\n",
      "Step=  134, Dmax= 4.4e-02 nm, Epot= -5.77359e+04 Fmax= 3.85366e+02, atom= 285\n",
      "Step=  135, Dmax= 5.3e-02 nm, Epot= -5.77624e+04 Fmax= 7.50828e+02, atom= 285\n",
      "Step=  136, Dmax= 6.4e-02 nm, Epot= -5.77981e+04 Fmax= 4.54376e+02, atom= 285\n",
      "Step=  138, Dmax= 3.8e-02 nm, Epot= -5.78377e+04 Fmax= 1.40492e+02, atom= 5043\n",
      "Step=  139, Dmax= 4.6e-02 nm, Epot= -5.78694e+04 Fmax= 7.93461e+02, atom= 4635\n",
      "Step=  140, Dmax= 5.5e-02 nm, Epot= -5.79361e+04 Fmax= 6.63909e+02, atom= 285\n",
      "Step=  141, Dmax= 6.6e-02 nm, Epot= -5.79552e+04 Fmax= 5.89226e+02, atom= 285\n",
      "Step=  142, Dmax= 7.9e-02 nm, Epot= -5.79725e+04 Fmax= 9.40391e+02, atom= 285\n",
      "Step=  143, Dmax= 9.5e-02 nm, Epot= -5.79907e+04 Fmax= 7.07770e+02, atom= 285\n",
      "Step=  145, Dmax= 5.7e-02 nm, Epot= -5.80467e+04 Fmax= 2.48711e+02, atom= 5043\n",
      "Step=  147, Dmax= 3.4e-02 nm, Epot= -5.80828e+04 Fmax= 1.80194e+02, atom= 4634\n",
      "Step=  149, Dmax= 2.1e-02 nm, Epot= -5.81124e+04 Fmax= 1.76968e+02, atom= 4634\n",
      "Step=  150, Dmax= 2.5e-02 nm, Epot= -5.81382e+04 Fmax= 2.74294e+02, atom= 2558\n",
      "Step=  151, Dmax= 3.0e-02 nm, Epot= -5.81669e+04 Fmax= 2.65196e+02, atom= 2558\n",
      "Step=  152, Dmax= 3.5e-02 nm, Epot= -5.81878e+04 Fmax= 3.79214e+02, atom= 2558\n",
      "Step=  153, Dmax= 4.3e-02 nm, Epot= -5.82143e+04 Fmax= 3.92706e+02, atom= 2558\n",
      "Step=  154, Dmax= 5.1e-02 nm, Epot= -5.82281e+04 Fmax= 5.24798e+02, atom= 2558\n",
      "Step=  155, Dmax= 6.1e-02 nm, Epot= -5.82503e+04 Fmax= 5.79046e+02, atom= 2558\n",
      "Step=  156, Dmax= 7.4e-02 nm, Epot= -5.82509e+04 Fmax= 7.28714e+02, atom= 2558\n",
      "Step=  157, Dmax= 8.8e-02 nm, Epot= -5.82588e+04 Fmax= 8.45931e+02, atom= 2558\n",
      "Step=  159, Dmax= 5.3e-02 nm, Epot= -5.83439e+04 Fmax= 2.05454e+02, atom= 2858\n",
      "Step=  160, Dmax= 6.4e-02 nm, Epot= -5.83443e+04 Fmax= 1.29098e+03, atom= 285\n",
      "Step=  161, Dmax= 7.6e-02 nm, Epot= -5.84063e+04 Fmax= 3.91486e+02, atom= 4635\n",
      "Step=  163, Dmax= 4.6e-02 nm, Epot= -5.84326e+04 Fmax= 2.44490e+02, atom= 285\n",
      "Step=  165, Dmax= 2.7e-02 nm, Epot= -5.84581e+04 Fmax= 2.18521e+02, atom= 2855\n",
      "Step=  166, Dmax= 3.3e-02 nm, Epot= -5.84788e+04 Fmax= 2.95386e+02, atom= 285\n",
      "Step=  167, Dmax= 4.0e-02 nm, Epot= -5.84927e+04 Fmax= 3.83630e+02, atom= 2558\n",
      "Step=  168, Dmax= 4.7e-02 nm, Epot= -5.85106e+04 Fmax= 4.59339e+02, atom= 2558\n",
      "Step=  169, Dmax= 5.7e-02 nm, Epot= -5.85206e+04 Fmax= 5.41944e+02, atom= 2558\n",
      "Step=  170, Dmax= 6.8e-02 nm, Epot= -5.85312e+04 Fmax= 6.62982e+02, atom= 2558\n",
      "Step=  172, Dmax= 4.1e-02 nm, Epot= -5.85911e+04 Fmax= 1.11736e+02, atom= 2858\n",
      "Step=  173, Dmax= 4.9e-02 nm, Epot= -5.86252e+04 Fmax= 8.80132e+02, atom= 285\n",
      "Step=  174, Dmax= 5.9e-02 nm, Epot= -5.86674e+04 Fmax= 2.93543e+02, atom= 285\n",
      "Step=  176, Dmax= 3.5e-02 nm, Epot= -5.86879e+04 Fmax= 2.57437e+02, atom= 285\n",
      "Step=  177, Dmax= 4.3e-02 nm, Epot= -5.86965e+04 Fmax= 4.14149e+02, atom= 285\n",
      "Step=  178, Dmax= 5.1e-02 nm, Epot= -5.87122e+04 Fmax= 4.88773e+02, atom= 285\n",
      "Step=  179, Dmax= 6.1e-02 nm, Epot= -5.87183e+04 Fmax= 5.02784e+02, atom= 285\n",
      "Step=  181, Dmax= 3.7e-02 nm, Epot= -5.87685e+04 Fmax= 1.24716e+02, atom= 2558\n",
      "Step=  182, Dmax= 4.4e-02 nm, Epot= -5.87783e+04 Fmax= 6.32760e+02, atom= 2558\n",
      "Step=  183, Dmax= 5.3e-02 nm, Epot= -5.88269e+04 Fmax= 2.78799e+02, atom= 2558\n",
      "Step=  185, Dmax= 3.2e-02 nm, Epot= -5.88438e+04 Fmax= 2.67023e+02, atom= 2558\n",
      "Step=  186, Dmax= 3.8e-02 nm, Epot= -5.88562e+04 Fmax= 3.92228e+02, atom= 2558\n",
      "Step=  187, Dmax= 4.6e-02 nm, Epot= -5.88719e+04 Fmax= 3.94399e+02, atom= 2558\n",
      "Step=  188, Dmax= 5.5e-02 nm, Epot= -5.88777e+04 Fmax= 5.51790e+02, atom= 2558\n",
      "Step=  189, Dmax= 6.6e-02 nm, Epot= -5.88898e+04 Fmax= 5.74763e+02, atom= 2558\n",
      "Step=  191, Dmax= 3.9e-02 nm, Epot= -5.89313e+04 Fmax= 9.24066e+01, atom= 2558\n",
      "Step=  192, Dmax= 4.7e-02 nm, Epot= -5.89464e+04 Fmax= 7.09055e+02, atom= 2558\n",
      "Step=  193, Dmax= 5.7e-02 nm, Epot= -5.89983e+04 Fmax= 2.72586e+02, atom= 2558\n",
      "Step=  195, Dmax= 3.4e-02 nm, Epot= -5.90113e+04 Fmax= 3.12088e+02, atom= 2558\n",
      "Step=  196, Dmax= 4.1e-02 nm, Epot= -5.90177e+04 Fmax= 3.89366e+02, atom= 2558\n",
      "Step=  197, Dmax= 4.9e-02 nm, Epot= -5.90259e+04 Fmax= 4.71057e+02, atom= 2750\n",
      "Step=  199, Dmax= 2.9e-02 nm, Epot= -5.90633e+04 Fmax= 1.07989e+02, atom= 2750\n",
      "Step=  200, Dmax= 3.5e-02 nm, Epot= -5.90842e+04 Fmax= 6.97884e+02, atom= 2750\n",
      "Step=  201, Dmax= 4.2e-02 nm, Epot= -5.91077e+04 Fmax= 1.90523e+02, atom= 2750\n",
      "Step=  203, Dmax= 2.5e-02 nm, Epot= -5.91226e+04 Fmax= 2.20171e+02, atom= 2750\n",
      "Step=  204, Dmax= 3.1e-02 nm, Epot= -5.91348e+04 Fmax= 2.94176e+02, atom= 2750\n",
      "Step=  205, Dmax= 3.7e-02 nm, Epot= -5.91476e+04 Fmax= 3.56281e+02, atom= 2750\n",
      "Step=  206, Dmax= 4.4e-02 nm, Epot= -5.91563e+04 Fmax= 3.82359e+02, atom= 2750\n",
      "Step=  207, Dmax= 5.3e-02 nm, Epot= -5.91628e+04 Fmax= 5.88973e+02, atom= 2750\n",
      "Step=  208, Dmax= 6.3e-02 nm, Epot= -5.91732e+04 Fmax= 4.85093e+02, atom= 2750\n",
      "Step=  210, Dmax= 3.8e-02 nm, Epot= -5.92039e+04 Fmax= 1.35743e+02, atom= 1037\n",
      "Step=  211, Dmax= 4.6e-02 nm, Epot= -5.92141e+04 Fmax= 5.65706e+02, atom= 1037\n",
      "Step=  212, Dmax= 5.5e-02 nm, Epot= -5.92410e+04 Fmax= 4.54354e+02, atom= 1037\n",
      "Step=  214, Dmax= 3.3e-02 nm, Epot= -5.92579e+04 Fmax= 1.66848e+02, atom= 2750\n",
      "Step=  215, Dmax= 3.9e-02 nm, Epot= -5.92647e+04 Fmax= 6.44873e+02, atom= 2750\n",
      "Step=  216, Dmax= 4.7e-02 nm, Epot= -5.92871e+04 Fmax= 2.43525e+02, atom= 2750\n",
      "Step=  218, Dmax= 2.8e-02 nm, Epot= -5.93006e+04 Fmax= 1.95952e+02, atom= 2750\n",
      "Step=  219, Dmax= 3.4e-02 nm, Epot= -5.93089e+04 Fmax= 3.67029e+02, atom= 2750\n",
      "Step=  220, Dmax= 4.1e-02 nm, Epot= -5.93240e+04 Fmax= 3.34144e+02, atom= 2750\n",
      "Step=  221, Dmax= 4.9e-02 nm, Epot= -5.93247e+04 Fmax= 4.66065e+02, atom= 1037\n",
      "Step=  222, Dmax= 5.9e-02 nm, Epot= -5.93346e+04 Fmax= 5.60595e+02, atom= 1037\n",
      "Step=  224, Dmax= 3.5e-02 nm, Epot= -5.93648e+04 Fmax= 1.09633e+02, atom= 2750\n",
      "Step=  225, Dmax= 4.2e-02 nm, Epot= -5.93780e+04 Fmax= 8.31451e+02, atom= 2750\n",
      "Step=  226, Dmax= 5.1e-02 nm, Epot= -5.94053e+04 Fmax= 2.09115e+02, atom= 2750\n",
      "Step=  228, Dmax= 3.1e-02 nm, Epot= -5.94176e+04 Fmax= 2.62302e+02, atom= 2750\n",
      "Step=  229, Dmax= 3.7e-02 nm, Epot= -5.94262e+04 Fmax= 3.36118e+02, atom= 2750\n",
      "Step=  230, Dmax= 4.4e-02 nm, Epot= -5.94357e+04 Fmax= 4.10895e+02, atom= 2750\n",
      "Step=  231, Dmax= 5.3e-02 nm, Epot= -5.94403e+04 Fmax= 4.45711e+02, atom= 2750\n",
      "Step=  233, Dmax= 3.2e-02 nm, Epot= -5.94655e+04 Fmax= 7.20466e+01, atom= 1037\n",
      "Step=  234, Dmax= 3.8e-02 nm, Epot= -5.94950e+04 Fmax= 4.87951e+02, atom= 1037\n",
      "Step=  235, Dmax= 4.6e-02 nm, Epot= -5.95155e+04 Fmax= 3.33452e+02, atom= 1037\n",
      "Step=  237, Dmax= 2.7e-02 nm, Epot= -5.95271e+04 Fmax= 1.38156e+02, atom= 2750\n",
      "Step=  238, Dmax= 3.3e-02 nm, Epot= -5.95330e+04 Fmax= 5.13054e+02, atom= 2750\n",
      "Step=  239, Dmax= 3.9e-02 nm, Epot= -5.95524e+04 Fmax= 2.04268e+02, atom= 2750\n",
      "Step=  241, Dmax= 2.4e-02 nm, Epot= -5.95633e+04 Fmax= 1.66953e+02, atom= 2750\n",
      "Step=  242, Dmax= 2.8e-02 nm, Epot= -5.95715e+04 Fmax= 2.97517e+02, atom= 2750\n",
      "Step=  243, Dmax= 3.4e-02 nm, Epot= -5.95832e+04 Fmax= 2.83477e+02, atom= 1037\n",
      "Step=  244, Dmax= 4.1e-02 nm, Epot= -5.95869e+04 Fmax= 3.94152e+02, atom= 1037\n",
      "Step=  245, Dmax= 4.9e-02 nm, Epot= -5.95965e+04 Fmax= 4.43375e+02, atom= 1037\n",
      "Step=  247, Dmax= 2.9e-02 nm, Epot= -5.96171e+04 Fmax= 8.59002e+01, atom= 2750\n",
      "Step=  248, Dmax= 3.5e-02 nm, Epot= -5.96313e+04 Fmax= 6.37273e+02, atom= 2750\n",
      "Step=  249, Dmax= 4.2e-02 nm, Epot= -5.96541e+04 Fmax= 1.76496e+02, atom= 2750\n",
      "Step=  251, Dmax= 2.5e-02 nm, Epot= -5.96643e+04 Fmax= 2.22371e+02, atom= 2750\n",
      "Step=  252, Dmax= 3.0e-02 nm, Epot= -5.96723e+04 Fmax= 2.74291e+02, atom= 2750\n",
      "Step=  253, Dmax= 3.7e-02 nm, Epot= -5.96804e+04 Fmax= 3.39338e+02, atom= 2750\n",
      "Step=  254, Dmax= 4.4e-02 nm, Epot= -5.96857e+04 Fmax= 3.71865e+02, atom= 2750\n",
      "Step=  255, Dmax= 5.3e-02 nm, Epot= -5.96876e+04 Fmax= 5.34522e+02, atom= 2750\n",
      "Step=  256, Dmax= 6.3e-02 nm, Epot= -5.96929e+04 Fmax= 4.90829e+02, atom= 2750\n",
      "Step=  258, Dmax= 3.8e-02 nm, Epot= -5.97230e+04 Fmax= 1.29100e+02, atom= 1037\n",
      "Step=  259, Dmax= 4.5e-02 nm, Epot= -5.97247e+04 Fmax= 5.78329e+02, atom= 1037\n",
      "Step=  260, Dmax= 5.5e-02 nm, Epot= -5.97496e+04 Fmax= 3.53992e+02, atom= 1037\n",
      "Step=  262, Dmax= 3.3e-02 nm, Epot= -5.97610e+04 Fmax= 1.91255e+02, atom= 1037\n",
      "Step=  264, Dmax= 2.0e-02 nm, Epot= -5.97701e+04 Fmax= 1.35681e+02, atom= 1037\n",
      "Step=  265, Dmax= 2.4e-02 nm, Epot= -5.97786e+04 Fmax= 2.54210e+02, atom= 1037\n",
      "Step=  266, Dmax= 2.8e-02 nm, Epot= -5.97881e+04 Fmax= 2.22014e+02, atom= 1037\n",
      "Step=  267, Dmax= 3.4e-02 nm, Epot= -5.97931e+04 Fmax= 3.36883e+02, atom= 1037\n",
      "Step=  268, Dmax= 4.1e-02 nm, Epot= -5.98018e+04 Fmax= 3.49815e+02, atom= 1037\n",
      "Step=  269, Dmax= 4.9e-02 nm, Epot= -5.98032e+04 Fmax= 4.53508e+02, atom= 1037\n",
      "Step=  270, Dmax= 5.9e-02 nm, Epot= -5.98085e+04 Fmax= 5.35072e+02, atom= 1037\n",
      "Step=  272, Dmax= 3.5e-02 nm, Epot= -5.98330e+04 Fmax= 8.22722e+01, atom= 2750\n",
      "Step=  273, Dmax= 4.2e-02 nm, Epot= -5.98371e+04 Fmax= 8.31920e+02, atom= 2750\n",
      "Step=  274, Dmax= 5.1e-02 nm, Epot= -5.98695e+04 Fmax= 1.78990e+02, atom= 2750\n",
      "Step=  276, Dmax= 3.0e-02 nm, Epot= -5.98776e+04 Fmax= 2.87462e+02, atom= 2750\n",
      "Step=  277, Dmax= 3.6e-02 nm, Epot= -5.98843e+04 Fmax= 3.00568e+02, atom= 2750\n",
      "Step=  278, Dmax= 4.4e-02 nm, Epot= -5.98884e+04 Fmax= 4.18449e+02, atom= 2750\n",
      "Step=  279, Dmax= 5.3e-02 nm, Epot= -5.98928e+04 Fmax= 4.22419e+02, atom= 2750\n",
      "Step=  281, Dmax= 3.2e-02 nm, Epot= -5.99127e+04 Fmax= 8.00841e+01, atom= 1037\n",
      "Step=  282, Dmax= 3.8e-02 nm, Epot= -5.99217e+04 Fmax= 5.07395e+02, atom= 1037\n",
      "Step=  283, Dmax= 4.5e-02 nm, Epot= -5.99439e+04 Fmax= 2.62831e+02, atom= 1037\n",
      "Step=  285, Dmax= 2.7e-02 nm, Epot= -5.99519e+04 Fmax= 1.83905e+02, atom= 1037\n",
      "Step=  286, Dmax= 3.3e-02 nm, Epot= -5.99549e+04 Fmax= 3.78590e+02, atom= 1037\n",
      "Step=  287, Dmax= 3.9e-02 nm, Epot= -5.99652e+04 Fmax= 2.74147e+02, atom= 1037\n",
      "Step=  289, Dmax= 2.4e-02 nm, Epot= -5.99761e+04 Fmax= 1.13455e+02, atom= 1037\n",
      "Step=  290, Dmax= 2.8e-02 nm, Epot= -5.99826e+04 Fmax= 3.45366e+02, atom= 1037\n",
      "Step=  291, Dmax= 3.4e-02 nm, Epot= -5.99945e+04 Fmax= 2.19360e+02, atom= 1037\n",
      "Step=  293, Dmax= 2.0e-02 nm, Epot= -6.00023e+04 Fmax= 1.17656e+02, atom= 1037\n",
      "Step=  294, Dmax= 2.4e-02 nm, Epot= -6.00091e+04 Fmax= 3.00515e+02, atom= 1037\n",
      "Step=  295, Dmax= 2.9e-02 nm, Epot= -6.00184e+04 Fmax= 1.87183e+02, atom= 1037\n",
      "Step=  296, Dmax= 3.5e-02 nm, Epot= -6.00195e+04 Fmax= 4.17089e+02, atom= 1037\n",
      "Step=  297, Dmax= 4.2e-02 nm, Epot= -6.00310e+04 Fmax= 2.84840e+02, atom= 1037\n",
      "Step=  299, Dmax= 2.5e-02 nm, Epot= -6.00418e+04 Fmax= 1.31955e+02, atom= 1037\n",
      "Step=  300, Dmax= 3.0e-02 nm, Epot= -6.00463e+04 Fmax= 3.60137e+02, atom= 1037\n",
      "Step=  301, Dmax= 3.6e-02 nm, Epot= -6.00579e+04 Fmax= 2.45266e+02, atom= 1037\n",
      "Step=  303, Dmax= 2.2e-02 nm, Epot= -6.00661e+04 Fmax= 1.16807e+02, atom= 1037\n",
      "Step=  304, Dmax= 2.6e-02 nm, Epot= -6.00720e+04 Fmax= 3.33042e+02, atom= 1037\n",
      "Step=  305, Dmax= 3.1e-02 nm, Epot= -6.00822e+04 Fmax= 1.91207e+02, atom= 1037\n",
      "Step=  307, Dmax= 1.9e-02 nm, Epot= -6.00896e+04 Fmax= 1.22868e+02, atom= 1037\n",
      "Step=  308, Dmax= 2.3e-02 nm, Epot= -6.00962e+04 Fmax= 2.45731e+02, atom= 1037\n",
      "Step=  309, Dmax= 2.7e-02 nm, Epot= -6.01039e+04 Fmax= 2.08716e+02, atom= 1037\n",
      "Step=  310, Dmax= 3.3e-02 nm, Epot= -6.01076e+04 Fmax= 3.23587e+02, atom= 1037\n",
      "Step=  311, Dmax= 3.9e-02 nm, Epot= -6.01146e+04 Fmax= 3.30965e+02, atom= 1037\n",
      "Step=  312, Dmax= 4.7e-02 nm, Epot= -6.01152e+04 Fmax= 4.35908e+02, atom= 1037\n",
      "Step=  313, Dmax= 5.6e-02 nm, Epot= -6.01193e+04 Fmax= 5.06340e+02, atom= 1037\n",
      "Step=  315, Dmax= 3.4e-02 nm, Epot= -6.01402e+04 Fmax= 6.74224e+01, atom= 2750\n",
      "Step=  317, Dmax= 2.0e-02 nm, Epot= -6.01506e+04 Fmax= 2.75903e+02, atom= 1037\n",
      "Step=  318, Dmax= 2.4e-02 nm, Epot= -6.01599e+04 Fmax= 1.34990e+02, atom= 1037\n",
      "Step=  319, Dmax= 2.9e-02 nm, Epot= -6.01621e+04 Fmax= 3.70568e+02, atom= 1037\n",
      "Step=  320, Dmax= 3.5e-02 nm, Epot= -6.01737e+04 Fmax= 2.16357e+02, atom= 1037\n",
      "Step=  322, Dmax= 2.1e-02 nm, Epot= -6.01817e+04 Fmax= 1.31919e+02, atom= 1037\n",
      "Step=  323, Dmax= 2.5e-02 nm, Epot= -6.01867e+04 Fmax= 2.79645e+02, atom= 1037\n",
      "Step=  324, Dmax= 3.0e-02 nm, Epot= -6.01951e+04 Fmax= 2.25485e+02, atom= 1037\n",
      "Step=  325, Dmax= 3.6e-02 nm, Epot= -6.01964e+04 Fmax= 3.67171e+02, atom= 1037\n",
      "Step=  326, Dmax= 4.4e-02 nm, Epot= -6.02041e+04 Fmax= 3.60232e+02, atom= 1037\n",
      "Step=  328, Dmax= 2.6e-02 nm, Epot= -6.02166e+04 Fmax= 7.92455e+01, atom= 1037\n",
      "Step=  329, Dmax= 3.1e-02 nm, Epot= -6.02207e+04 Fmax= 4.79290e+02, atom= 1037\n",
      "Step=  330, Dmax= 3.8e-02 nm, Epot= -6.02388e+04 Fmax= 1.65514e+02, atom= 1037\n",
      "Step=  332, Dmax= 2.3e-02 nm, Epot= -6.02444e+04 Fmax= 2.13497e+02, atom= 1037\n",
      "Step=  333, Dmax= 2.7e-02 nm, Epot= -6.02497e+04 Fmax= 2.34472e+02, atom= 1037\n",
      "Step=  334, Dmax= 3.3e-02 nm, Epot= -6.02538e+04 Fmax= 3.14438e+02, atom= 1037\n",
      "Step=  335, Dmax= 3.9e-02 nm, Epot= -6.02584e+04 Fmax= 3.29824e+02, atom= 1037\n",
      "Step=  336, Dmax= 4.7e-02 nm, Epot= -6.02588e+04 Fmax= 4.61035e+02, atom= 1037\n",
      "Step=  337, Dmax= 5.6e-02 nm, Epot= -6.02622e+04 Fmax= 4.64117e+02, atom= 1037\n",
      "Step=  339, Dmax= 3.4e-02 nm, Epot= -6.02836e+04 Fmax= 8.26266e+01, atom= 1037\n",
      "Step=  340, Dmax= 4.1e-02 nm, Epot= -6.02865e+04 Fmax= 5.54988e+02, atom= 1037\n",
      "Step=  341, Dmax= 4.9e-02 nm, Epot= -6.03081e+04 Fmax= 2.47292e+02, atom= 1037\n",
      "Step=  343, Dmax= 2.9e-02 nm, Epot= -6.03138e+04 Fmax= 2.30271e+02, atom= 1037\n",
      "Step=  344, Dmax= 3.5e-02 nm, Epot= -6.03161e+04 Fmax= 3.58030e+02, atom= 1037\n",
      "Step=  345, Dmax= 4.2e-02 nm, Epot= -6.03217e+04 Fmax= 3.34048e+02, atom= 1037\n",
      "Step=  347, Dmax= 2.5e-02 nm, Epot= -6.03334e+04 Fmax= 7.76801e+01, atom= 1037\n",
      "Step=  348, Dmax= 3.0e-02 nm, Epot= -6.03398e+04 Fmax= 4.07179e+02, atom= 1037\n",
      "Step=  349, Dmax= 3.6e-02 nm, Epot= -6.03535e+04 Fmax= 1.90604e+02, atom= 1037\n",
      "Step=  351, Dmax= 2.2e-02 nm, Epot= -6.03590e+04 Fmax= 1.67562e+02, atom= 1037\n",
      "Step=  352, Dmax= 2.6e-02 nm, Epot= -6.03628e+04 Fmax= 2.72241e+02, atom= 1037\n",
      "Step=  353, Dmax= 3.1e-02 nm, Epot= -6.03686e+04 Fmax= 2.45528e+02, atom= 1037\n",
      "Step=  354, Dmax= 3.8e-02 nm, Epot= -6.03690e+04 Fmax= 3.89593e+02, atom= 1037\n",
      "Step=  355, Dmax= 4.5e-02 nm, Epot= -6.03747e+04 Fmax= 3.56036e+02, atom= 1037\n",
      "Step=  357, Dmax= 2.7e-02 nm, Epot= -6.03881e+04 Fmax= 8.61068e+01, atom= 1037\n",
      "Step=  358, Dmax= 3.3e-02 nm, Epot= -6.03886e+04 Fmax= 4.35313e+02, atom= 1037\n",
      "Step=  359, Dmax= 3.9e-02 nm, Epot= -6.04053e+04 Fmax= 2.07639e+02, atom= 1037\n",
      "Step=  361, Dmax= 2.3e-02 nm, Epot= -6.04109e+04 Fmax= 1.78364e+02, atom= 1037\n",
      "Step=  362, Dmax= 2.8e-02 nm, Epot= -6.04121e+04 Fmax= 2.95268e+02, atom= 1037\n",
      "Step=  363, Dmax= 3.4e-02 nm, Epot= -6.04179e+04 Fmax= 2.62369e+02, atom= 1037\n",
      "Step=  365, Dmax= 2.0e-02 nm, Epot= -6.04286e+04 Fmax= 7.02098e+01, atom= 1037\n",
      "Step=  367, Dmax= 1.2e-02 nm, Epot= -6.04340e+04 Fmax= 1.27299e+02, atom= 1037\n",
      "Step=  368, Dmax= 1.5e-02 nm, Epot= -6.04391e+04 Fmax= 1.16376e+02, atom= 1037\n",
      "Step=  369, Dmax= 1.7e-02 nm, Epot= -6.04420e+04 Fmax= 1.70247e+02, atom= 1037\n",
      "Step=  370, Dmax= 2.1e-02 nm, Epot= -6.04457e+04 Fmax= 1.82795e+02, atom= 1949\n",
      "Step=  372, Dmax= 1.3e-02 nm, Epot= -6.04557e+04 Fmax= 3.24653e+01, atom= 1223\n",
      "Step=  373, Dmax= 1.5e-02 nm, Epot= -6.04636e+04 Fmax= 2.56892e+02, atom= 1223\n",
      "Step=  374, Dmax= 1.8e-02 nm, Epot= -6.04776e+04 Fmax= 7.03043e+01, atom= 1223\n",
      "Step=  376, Dmax= 1.1e-02 nm, Epot= -6.04828e+04 Fmax= 1.18501e+02, atom= 1223\n",
      "Step=  377, Dmax= 1.3e-02 nm, Epot= -6.04876e+04 Fmax= 1.07331e+02, atom= 1223\n",
      "Step=  378, Dmax= 1.6e-02 nm, Epot= -6.04915e+04 Fmax= 1.70629e+02, atom= 1223\n",
      "Step=  379, Dmax= 1.9e-02 nm, Epot= -6.04965e+04 Fmax= 1.56634e+02, atom= 1223\n",
      "Step=  380, Dmax= 2.3e-02 nm, Epot= -6.04986e+04 Fmax= 2.41043e+02, atom= 1223\n",
      "Step=  381, Dmax= 2.7e-02 nm, Epot= -6.05037e+04 Fmax= 2.29850e+02, atom= 1223\n",
      "Step=  383, Dmax= 1.6e-02 nm, Epot= -6.05126e+04 Fmax= 5.26314e+01, atom= 1223\n",
      "Step=  384, Dmax= 1.9e-02 nm, Epot= -6.05193e+04 Fmax= 2.92343e+02, atom= 1223\n",
      "Step=  385, Dmax= 2.3e-02 nm, Epot= -6.05295e+04 Fmax= 1.30780e+02, atom= 1223\n",
      "Step=  387, Dmax= 1.4e-02 nm, Epot= -6.05342e+04 Fmax= 1.05053e+02, atom= 1223\n",
      "Step=  388, Dmax= 1.7e-02 nm, Epot= -6.05381e+04 Fmax= 1.89563e+02, atom= 1223\n",
      "Step=  389, Dmax= 2.0e-02 nm, Epot= -6.05433e+04 Fmax= 1.57603e+02, atom= 1223\n",
      "Step=  390, Dmax= 2.4e-02 nm, Epot= -6.05448e+04 Fmax= 2.65033e+02, atom= 1223\n",
      "Step=  391, Dmax= 2.9e-02 nm, Epot= -6.05503e+04 Fmax= 2.37203e+02, atom= 1223\n",
      "Step=  393, Dmax= 1.7e-02 nm, Epot= -6.05586e+04 Fmax= 6.57889e+01, atom= 1223\n",
      "Step=  394, Dmax= 2.1e-02 nm, Epot= -6.05627e+04 Fmax= 3.05352e+02, atom= 1223\n",
      "Step=  395, Dmax= 2.5e-02 nm, Epot= -6.05727e+04 Fmax= 1.44005e+02, atom= 1223\n",
      "Step=  397, Dmax= 1.5e-02 nm, Epot= -6.05773e+04 Fmax= 1.08536e+02, atom= 1223\n",
      "Step=  398, Dmax= 1.8e-02 nm, Epot= -6.05807e+04 Fmax= 2.07503e+02, atom= 1223\n",
      "Step=  399, Dmax= 2.2e-02 nm, Epot= -6.05861e+04 Fmax= 1.64592e+02, atom= 1223\n",
      "Step=  400, Dmax= 2.6e-02 nm, Epot= -6.05864e+04 Fmax= 2.88908e+02, atom= 1223\n",
      "Step=  401, Dmax= 3.1e-02 nm, Epot= -6.05924e+04 Fmax= 2.49418e+02, atom= 1223\n",
      "Step=  403, Dmax= 1.9e-02 nm, Epot= -6.06012e+04 Fmax= 7.42693e+01, atom= 1223\n",
      "Step=  404, Dmax= 2.3e-02 nm, Epot= -6.06030e+04 Fmax= 3.24604e+02, atom= 1223\n",
      "Step=  405, Dmax= 2.7e-02 nm, Epot= -6.06140e+04 Fmax= 1.57066e+02, atom= 1223\n",
      "Step=  407, Dmax= 1.6e-02 nm, Epot= -6.06188e+04 Fmax= 1.13301e+02, atom= 1223\n",
      "Step=  408, Dmax= 1.9e-02 nm, Epot= -6.06213e+04 Fmax= 2.26259e+02, atom= 1223\n",
      "Step=  409, Dmax= 2.3e-02 nm, Epot= -6.06271e+04 Fmax= 1.72987e+02, atom= 1223\n",
      "Step=  411, Dmax= 1.4e-02 nm, Epot= -6.06328e+04 Fmax= 6.94849e+01, atom= 1223\n",
      "Step=  412, Dmax= 1.7e-02 nm, Epot= -6.06371e+04 Fmax= 2.19846e+02, atom= 1223\n",
      "Step=  413, Dmax= 2.0e-02 nm, Epot= -6.06437e+04 Fmax= 1.33677e+02, atom= 1223\n",
      "Step=  414, Dmax= 2.4e-02 nm, Epot= -6.06437e+04 Fmax= 2.86011e+02, atom= 1223\n",
      "Step=  415, Dmax= 2.9e-02 nm, Epot= -6.06508e+04 Fmax= 2.16489e+02, atom= 1223\n",
      "Step=  417, Dmax= 1.7e-02 nm, Epot= -6.06582e+04 Fmax= 7.43573e+01, atom= 1223\n",
      "Step=  418, Dmax= 2.1e-02 nm, Epot= -6.06584e+04 Fmax= 3.06738e+02, atom= 1223\n",
      "Step=  419, Dmax= 2.5e-02 nm, Epot= -6.06699e+04 Fmax= 1.31746e+02, atom= 1223\n",
      "Step=  421, Dmax= 1.5e-02 nm, Epot= -6.06743e+04 Fmax= 1.24125e+02, atom= 1223\n",
      "Step=  422, Dmax= 1.8e-02 nm, Epot= -6.06772e+04 Fmax= 1.85336e+02, atom= 1223\n",
      "Step=  423, Dmax= 2.2e-02 nm, Epot= -6.06812e+04 Fmax= 1.91020e+02, atom= 1223\n",
      "Step=  424, Dmax= 2.6e-02 nm, Epot= -6.06825e+04 Fmax= 2.56809e+02, atom= 1223\n",
      "Step=  425, Dmax= 3.1e-02 nm, Epot= -6.06852e+04 Fmax= 2.81063e+02, atom= 1223\n",
      "Step=  427, Dmax= 1.9e-02 nm, Epot= -6.06969e+04 Fmax= 5.07303e+01, atom= 2326\n",
      "Step=  428, Dmax= 2.2e-02 nm, Epot= -6.07028e+04 Fmax= 3.54027e+02, atom= 2326\n",
      "Step=  429, Dmax= 2.7e-02 nm, Epot= -6.07137e+04 Fmax= 1.30348e+02, atom= 1223\n",
      "Step=  431, Dmax= 1.6e-02 nm, Epot= -6.07179e+04 Fmax= 1.33923e+02, atom= 1223\n",
      "Step=  432, Dmax= 1.9e-02 nm, Epot= -6.07204e+04 Fmax= 1.96251e+02, atom= 1223\n",
      "Step=  433, Dmax= 2.3e-02 nm, Epot= -6.07244e+04 Fmax= 2.06369e+02, atom= 1223\n",
      "Step=  434, Dmax= 2.8e-02 nm, Epot= -6.07254e+04 Fmax= 2.73626e+02, atom= 1223\n",
      "Step=  435, Dmax= 3.4e-02 nm, Epot= -6.07282e+04 Fmax= 3.02467e+02, atom= 1223\n",
      "Step=  437, Dmax= 2.0e-02 nm, Epot= -6.07402e+04 Fmax= 6.05849e+01, atom= 2326\n",
      "Step=  438, Dmax= 2.4e-02 nm, Epot= -6.07457e+04 Fmax= 3.65725e+02, atom= 2326\n",
      "Step=  439, Dmax= 2.9e-02 nm, Epot= -6.07549e+04 Fmax= 1.42202e+02, atom= 2326\n",
      "Step=  441, Dmax= 1.7e-02 nm, Epot= -6.07592e+04 Fmax= 1.38473e+02, atom= 1223\n",
      "Step=  442, Dmax= 2.1e-02 nm, Epot= -6.07611e+04 Fmax= 2.15298e+02, atom= 1223\n",
      "Step=  443, Dmax= 2.5e-02 nm, Epot= -6.07657e+04 Fmax= 2.15387e+02, atom= 1223\n",
      "Step=  445, Dmax= 1.5e-02 nm, Epot= -6.07728e+04 Fmax= 5.21423e+01, atom= 2326\n",
      "Step=  446, Dmax= 1.8e-02 nm, Epot= -6.07796e+04 Fmax= 2.56476e+02, atom= 2326\n",
      "Step=  447, Dmax= 2.2e-02 nm, Epot= -6.07864e+04 Fmax= 1.17198e+02, atom= 1223\n",
      "Step=  449, Dmax= 1.3e-02 nm, Epot= -6.07907e+04 Fmax= 9.99643e+01, atom= 1223\n",
      "Step=  450, Dmax= 1.6e-02 nm, Epot= -6.07940e+04 Fmax= 1.64265e+02, atom= 1223\n",
      "Step=  451, Dmax= 1.9e-02 nm, Epot= -6.07984e+04 Fmax= 1.60225e+02, atom= 1223\n",
      "Step=  452, Dmax= 2.2e-02 nm, Epot= -6.08005e+04 Fmax= 2.22581e+02, atom= 1223\n",
      "Step=  453, Dmax= 2.7e-02 nm, Epot= -6.08042e+04 Fmax= 2.41085e+02, atom= 1223\n",
      "Step=  454, Dmax= 3.2e-02 nm, Epot= -6.08045e+04 Fmax= 3.11641e+02, atom= 1223\n",
      "Step=  455, Dmax= 3.9e-02 nm, Epot= -6.08066e+04 Fmax= 3.48347e+02, atom= 1223\n",
      "Step=  457, Dmax= 2.3e-02 nm, Epot= -6.08208e+04 Fmax= 6.99340e+01, atom= 2326\n",
      "Step=  458, Dmax= 2.8e-02 nm, Epot= -6.08238e+04 Fmax= 4.30790e+02, atom= 2326\n",
      "Step=  459, Dmax= 3.4e-02 nm, Epot= -6.08347e+04 Fmax= 1.58143e+02, atom= 2326\n",
      "Step=  461, Dmax= 2.0e-02 nm, Epot= -6.08390e+04 Fmax= 1.59487e+02, atom= 2327\n",
      "Step=  462, Dmax= 2.4e-02 nm, Epot= -6.08398e+04 Fmax= 2.41392e+02, atom= 1223\n",
      "Step=  463, Dmax= 2.9e-02 nm, Epot= -6.08440e+04 Fmax= 2.52208e+02, atom= 1223\n",
      "Step=  465, Dmax= 1.7e-02 nm, Epot= -6.08533e+04 Fmax= 6.02601e+01, atom= 2326\n",
      "Step=  466, Dmax= 2.1e-02 nm, Epot= -6.08591e+04 Fmax= 2.91071e+02, atom= 2326\n",
      "Step=  467, Dmax= 2.5e-02 nm, Epot= -6.08663e+04 Fmax= 1.35117e+02, atom= 2326\n",
      "Step=  469, Dmax= 1.5e-02 nm, Epot= -6.08708e+04 Fmax= 1.09440e+02, atom= 2327\n",
      "Step=  470, Dmax= 1.8e-02 nm, Epot= -6.08733e+04 Fmax= 1.90966e+02, atom= 1223\n",
      "Step=  471, Dmax= 2.2e-02 nm, Epot= -6.08780e+04 Fmax= 1.81492e+02, atom= 1223\n",
      "Step=  472, Dmax= 2.6e-02 nm, Epot= -6.08789e+04 Fmax= 2.58389e+02, atom= 1223\n",
      "Step=  473, Dmax= 3.1e-02 nm, Epot= -6.08827e+04 Fmax= 2.73250e+02, atom= 1223\n",
      "Step=  475, Dmax= 1.9e-02 nm, Epot= -6.08927e+04 Fmax= 5.96241e+01, atom= 2326\n",
      "Step=  476, Dmax= 2.2e-02 nm, Epot= -6.08978e+04 Fmax= 3.29611e+02, atom= 2326\n",
      "Step=  477, Dmax= 2.7e-02 nm, Epot= -6.09063e+04 Fmax= 1.34986e+02, atom= 2326\n",
      "Step=  479, Dmax= 1.6e-02 nm, Epot= -6.09107e+04 Fmax= 1.24750e+02, atom= 2327\n",
      "Step=  480, Dmax= 1.9e-02 nm, Epot= -6.09128e+04 Fmax= 1.97233e+02, atom= 1223\n",
      "Step=  481, Dmax= 2.3e-02 nm, Epot= -6.09170e+04 Fmax= 2.01198e+02, atom= 1223\n",
      "Step=  482, Dmax= 2.8e-02 nm, Epot= -6.09176e+04 Fmax= 2.70444e+02, atom= 1223\n",
      "Step=  483, Dmax= 3.3e-02 nm, Epot= -6.09205e+04 Fmax= 2.98919e+02, atom= 1223\n",
      "Step=  485, Dmax= 2.0e-02 nm, Epot= -6.09324e+04 Fmax= 6.28237e+01, atom= 2326\n",
      "Step=  486, Dmax= 2.4e-02 nm, Epot= -6.09374e+04 Fmax= 3.51108e+02, atom= 2326\n",
      "Step=  487, Dmax= 2.9e-02 nm, Epot= -6.09460e+04 Fmax= 1.44706e+02, atom= 2326\n",
      "Step=  489, Dmax= 1.7e-02 nm, Epot= -6.09503e+04 Fmax= 1.35641e+02, atom= 2327\n",
      "Step=  490, Dmax= 2.1e-02 nm, Epot= -6.09523e+04 Fmax= 2.04670e+02, atom= 2327\n",
      "Step=  491, Dmax= 2.5e-02 nm, Epot= -6.09560e+04 Fmax= 2.16173e+02, atom= 1223\n",
      "Step=  493, Dmax= 1.5e-02 nm, Epot= -6.09637e+04 Fmax= 5.23354e+01, atom= 2326\n",
      "Step=  494, Dmax= 1.8e-02 nm, Epot= -6.09703e+04 Fmax= 2.48278e+02, atom= 2326\n",
      "Step=  495, Dmax= 2.2e-02 nm, Epot= -6.09767e+04 Fmax= 1.17648e+02, atom= 2326\n",
      "Step=  497, Dmax= 1.3e-02 nm, Epot= -6.09810e+04 Fmax= 9.57970e+01, atom= 2327\n",
      "Step=  498, Dmax= 1.6e-02 nm, Epot= -6.09842e+04 Fmax= 1.56906e+02, atom= 1223\n",
      "Step=  499, Dmax= 1.9e-02 nm, Epot= -6.09882e+04 Fmax= 1.64292e+02, atom= 1223\n",
      "Step=  500, Dmax= 2.2e-02 nm, Epot= -6.09903e+04 Fmax= 2.12035e+02, atom= 1223\n",
      "Step=  501, Dmax= 2.7e-02 nm, Epot= -6.09931e+04 Fmax= 2.46997e+02, atom= 1223\n",
      "Step=  502, Dmax= 3.2e-02 nm, Epot= -6.09936e+04 Fmax= 2.96341e+02, atom= 1223\n",
      "Step=  503, Dmax= 3.9e-02 nm, Epot= -6.09937e+04 Fmax= 3.56965e+02, atom= 1223\n",
      "Step=  505, Dmax= 2.3e-02 nm, Epot= -6.10108e+04 Fmax= 6.71921e+01, atom= 2326\n",
      "Step=  506, Dmax= 2.8e-02 nm, Epot= -6.10157e+04 Fmax= 4.04859e+02, atom= 2326\n",
      "Step=  507, Dmax= 3.3e-02 nm, Epot= -6.10247e+04 Fmax= 1.62177e+02, atom= 2326\n",
      "Step=  509, Dmax= 2.0e-02 nm, Epot= -6.10290e+04 Fmax= 1.63104e+02, atom= 2327\n",
      "Step=  510, Dmax= 2.4e-02 nm, Epot= -6.10306e+04 Fmax= 2.28723e+02, atom= 2327\n",
      "Step=  511, Dmax= 2.9e-02 nm, Epot= -6.10336e+04 Fmax= 2.46947e+02, atom= 2327\n",
      "Step=  513, Dmax= 1.7e-02 nm, Epot= -6.10428e+04 Fmax= 6.12178e+01, atom= 2326\n",
      "Step=  514, Dmax= 2.1e-02 nm, Epot= -6.10473e+04 Fmax= 2.91723e+02, atom= 2326\n",
      "Step=  515, Dmax= 2.5e-02 nm, Epot= -6.10550e+04 Fmax= 1.31883e+02, atom= 2326\n",
      "Step=  517, Dmax= 1.5e-02 nm, Epot= -6.10593e+04 Fmax= 1.15556e+02, atom= 2327\n",
      "Step=  518, Dmax= 1.8e-02 nm, Epot= -6.10619e+04 Fmax= 1.74574e+02, atom= 2327\n",
      "Step=  519, Dmax= 2.2e-02 nm, Epot= -6.10655e+04 Fmax= 1.83451e+02, atom= 2327\n",
      "Step=  520, Dmax= 2.6e-02 nm, Epot= -6.10659e+04 Fmax= 2.47827e+02, atom= 2327\n",
      "Step=  521, Dmax= 3.1e-02 nm, Epot= -6.10684e+04 Fmax= 2.73296e+02, atom= 1223\n",
      "Step=  523, Dmax= 1.9e-02 nm, Epot= -6.10802e+04 Fmax= 6.18504e+01, atom= 2326\n",
      "Step=  524, Dmax= 2.2e-02 nm, Epot= -6.10843e+04 Fmax= 3.14941e+02, atom= 2326\n",
      "Step=  525, Dmax= 2.7e-02 nm, Epot= -6.10925e+04 Fmax= 1.38163e+02, atom= 2326\n",
      "Step=  527, Dmax= 1.6e-02 nm, Epot= -6.10968e+04 Fmax= 1.27977e+02, atom= 2327\n",
      "Step=  528, Dmax= 1.9e-02 nm, Epot= -6.10990e+04 Fmax= 1.84856e+02, atom= 2327\n",
      "Step=  529, Dmax= 2.3e-02 nm, Epot= -6.11021e+04 Fmax= 1.99339e+02, atom= 2327\n",
      "Step=  531, Dmax= 1.4e-02 nm, Epot= -6.11093e+04 Fmax= 4.64262e+01, atom= 2326\n",
      "Step=  532, Dmax= 1.7e-02 nm, Epot= -6.11156e+04 Fmax= 2.30252e+02, atom= 2326\n",
      "Step=  533, Dmax= 2.0e-02 nm, Epot= -6.11221e+04 Fmax= 1.07528e+02, atom= 2326\n",
      "Step=  535, Dmax= 1.2e-02 nm, Epot= -6.11259e+04 Fmax= 9.38625e+01, atom= 2327\n",
      "Step=  536, Dmax= 1.4e-02 nm, Epot= -6.11291e+04 Fmax= 1.40430e+02, atom= 2327\n",
      "Step=  537, Dmax= 1.7e-02 nm, Epot= -6.11325e+04 Fmax= 1.48252e+02, atom= 2327\n",
      "Step=  538, Dmax= 2.1e-02 nm, Epot= -6.11340e+04 Fmax= 1.97714e+02, atom= 2327\n",
      "Step=  539, Dmax= 2.5e-02 nm, Epot= -6.11365e+04 Fmax= 2.16855e+02, atom= 1223\n",
      "Step=  541, Dmax= 1.5e-02 nm, Epot= -6.11456e+04 Fmax= 4.98271e+01, atom= 2326\n",
      "Step=  542, Dmax= 1.8e-02 nm, Epot= -6.11506e+04 Fmax= 2.48533e+02, atom= 2326\n",
      "Step=  543, Dmax= 2.2e-02 nm, Epot= -6.11577e+04 Fmax= 1.13798e+02, atom= 2326\n",
      "Step=  545, Dmax= 1.3e-02 nm, Epot= -6.11615e+04 Fmax= 1.02535e+02, atom= 2327\n",
      "Step=  546, Dmax= 1.5e-02 nm, Epot= -6.11641e+04 Fmax= 1.49348e+02, atom= 2327\n",
      "Step=  547, Dmax= 1.9e-02 nm, Epot= -6.11672e+04 Fmax= 1.60635e+02, atom= 2327\n",
      "Step=  548, Dmax= 2.2e-02 nm, Epot= -6.11681e+04 Fmax= 2.10958e+02, atom= 2327\n",
      "Step=  549, Dmax= 2.7e-02 nm, Epot= -6.11699e+04 Fmax= 2.31711e+02, atom= 2327\n",
      "Step=  551, Dmax= 1.6e-02 nm, Epot= -6.11808e+04 Fmax= 5.42368e+01, atom= 2326\n",
      "Step=  552, Dmax= 1.9e-02 nm, Epot= -6.11837e+04 Fmax= 2.69126e+02, atom= 2326\n",
      "Step=  553, Dmax= 2.3e-02 nm, Epot= -6.11920e+04 Fmax= 1.20699e+02, atom= 2326\n",
      "Step=  555, Dmax= 1.4e-02 nm, Epot= -6.11958e+04 Fmax= 1.12091e+02, atom= 2327\n",
      "Step=  556, Dmax= 1.7e-02 nm, Epot= -6.11980e+04 Fmax= 1.57795e+02, atom= 2327\n",
      "Step=  557, Dmax= 2.0e-02 nm, Epot= -6.12007e+04 Fmax= 1.74921e+02, atom= 2327\n",
      "Step=  558, Dmax= 2.4e-02 nm, Epot= -6.12009e+04 Fmax= 2.23417e+02, atom= 2327\n",
      "Step=  559, Dmax= 2.9e-02 nm, Epot= -6.12016e+04 Fmax= 2.51672e+02, atom= 2327\n",
      "Step=  561, Dmax= 1.7e-02 nm, Epot= -6.12149e+04 Fmax= 5.52209e+01, atom= 2326\n",
      "Step=  562, Dmax= 2.1e-02 nm, Epot= -6.12168e+04 Fmax= 2.93120e+02, atom= 2326\n",
      "Step=  563, Dmax= 2.5e-02 nm, Epot= -6.12263e+04 Fmax= 1.26087e+02, atom= 2326\n",
      "Step=  565, Dmax= 1.5e-02 nm, Epot= -6.12300e+04 Fmax= 1.24136e+02, atom= 2327\n",
      "Step=  566, Dmax= 1.8e-02 nm, Epot= -6.12320e+04 Fmax= 1.65719e+02, atom= 2327\n",
      "Step=  567, Dmax= 2.1e-02 nm, Epot= -6.12341e+04 Fmax= 1.91486e+02, atom= 2327\n",
      "Step=  568, Dmax= 2.6e-02 nm, Epot= -6.12342e+04 Fmax= 2.35788e+02, atom= 2327\n",
      "Step=  570, Dmax= 1.5e-02 nm, Epot= -6.12457e+04 Fmax= 3.28485e+01, atom= 1949\n",
      "Step=  571, Dmax= 1.9e-02 nm, Epot= -6.12528e+04 Fmax= 3.12952e+02, atom= 1949\n",
      "Step=  572, Dmax= 2.2e-02 nm, Epot= -6.12635e+04 Fmax= 8.37420e+01, atom= 1949\n",
      "Step=  574, Dmax= 1.3e-02 nm, Epot= -6.12669e+04 Fmax= 1.46378e+02, atom= 1949\n",
      "Step=  575, Dmax= 1.6e-02 nm, Epot= -6.12704e+04 Fmax= 1.24146e+02, atom= 1949\n",
      "Step=  576, Dmax= 1.9e-02 nm, Epot= -6.12724e+04 Fmax= 2.11671e+02, atom= 1949\n",
      "Step=  577, Dmax= 2.3e-02 nm, Epot= -6.12763e+04 Fmax= 1.78723e+02, atom= 1949\n",
      "Step=  579, Dmax= 1.4e-02 nm, Epot= -6.12815e+04 Fmax= 5.08404e+01, atom= 1949\n",
      "Step=  580, Dmax= 1.7e-02 nm, Epot= -6.12853e+04 Fmax= 2.25402e+02, atom= 1949\n",
      "Step=  581, Dmax= 2.0e-02 nm, Epot= -6.12922e+04 Fmax= 1.14717e+02, atom= 1949\n",
      "Step=  583, Dmax= 1.2e-02 nm, Epot= -6.12957e+04 Fmax= 8.96617e+01, atom= 1949\n",
      "Step=  584, Dmax= 1.4e-02 nm, Epot= -6.12986e+04 Fmax= 1.61616e+02, atom= 1949\n",
      "Step=  585, Dmax= 1.7e-02 nm, Epot= -6.13024e+04 Fmax= 1.31872e+02, atom= 1949\n",
      "Step=  586, Dmax= 2.1e-02 nm, Epot= -6.13036e+04 Fmax= 2.31553e+02, atom= 1949\n",
      "Step=  587, Dmax= 2.5e-02 nm, Epot= -6.13080e+04 Fmax= 1.89964e+02, atom= 1949\n",
      "Step=  589, Dmax= 1.5e-02 nm, Epot= -6.13136e+04 Fmax= 5.63080e+01, atom= 1949\n",
      "Step=  590, Dmax= 1.8e-02 nm, Epot= -6.13161e+04 Fmax= 2.41869e+02, atom= 1949\n",
      "Step=  591, Dmax= 2.1e-02 nm, Epot= -6.13239e+04 Fmax= 1.23513e+02, atom= 1949\n",
      "Step=  593, Dmax= 1.3e-02 nm, Epot= -6.13275e+04 Fmax= 9.63505e+01, atom= 1949\n",
      "Step=  594, Dmax= 1.5e-02 nm, Epot= -6.13300e+04 Fmax= 1.73277e+02, atom= 1949\n",
      "Step=  595, Dmax= 1.9e-02 nm, Epot= -6.13339e+04 Fmax= 1.42028e+02, atom= 1949\n",
      "Step=  596, Dmax= 2.2e-02 nm, Epot= -6.13347e+04 Fmax= 2.48073e+02, atom= 1949\n",
      "Step=  597, Dmax= 2.7e-02 nm, Epot= -6.13392e+04 Fmax= 2.04293e+02, atom= 1949\n",
      "Step=  599, Dmax= 1.6e-02 nm, Epot= -6.13453e+04 Fmax= 5.91080e+01, atom= 1949\n",
      "Step=  600, Dmax= 1.9e-02 nm, Epot= -6.13467e+04 Fmax= 2.61541e+02, atom= 1949\n",
      "Step=  601, Dmax= 2.3e-02 nm, Epot= -6.13554e+04 Fmax= 1.30293e+02, atom= 1949\n",
      "Step=  603, Dmax= 1.4e-02 nm, Epot= -6.13590e+04 Fmax= 1.05596e+02, atom= 1949\n",
      "Step=  604, Dmax= 1.7e-02 nm, Epot= -6.13612e+04 Fmax= 1.83230e+02, atom= 1949\n",
      "Step=  605, Dmax= 2.0e-02 nm, Epot= -6.13651e+04 Fmax= 1.54879e+02, atom= 1949\n",
      "Step=  606, Dmax= 2.4e-02 nm, Epot= -6.13653e+04 Fmax= 2.63165e+02, atom= 1949\n",
      "Step=  607, Dmax= 2.9e-02 nm, Epot= -6.13698e+04 Fmax= 2.21558e+02, atom= 1949\n",
      "Step=  609, Dmax= 1.7e-02 nm, Epot= -6.13767e+04 Fmax= 6.02873e+01, atom= 1949\n",
      "Step=  611, Dmax= 1.0e-02 nm, Epot= -6.13804e+04 Fmax= 1.15753e+02, atom= 1949\n",
      "Step=  612, Dmax= 1.2e-02 nm, Epot= -6.13838e+04 Fmax= 9.54349e+01, atom= 1949\n",
      "Step=  613, Dmax= 1.5e-02 nm, Epot= -6.13864e+04 Fmax= 1.54037e+02, atom= 1949\n",
      "Step=  614, Dmax= 1.8e-02 nm, Epot= -6.13899e+04 Fmax= 1.50894e+02, atom= 1949\n",
      "Step=  615, Dmax= 2.1e-02 nm, Epot= -6.13913e+04 Fmax= 2.07060e+02, atom= 1949\n",
      "Step=  616, Dmax= 2.6e-02 nm, Epot= -6.13939e+04 Fmax= 2.35138e+02, atom= 1949\n",
      "Step=  617, Dmax= 3.1e-02 nm, Epot= -6.13943e+04 Fmax= 2.78445e+02, atom= 1949\n",
      "Step=  619, Dmax= 1.8e-02 nm, Epot= -6.14049e+04 Fmax= 2.74896e+01, atom= 3323\n",
      "Step=  620, Dmax= 2.2e-02 nm, Epot= -6.14121e+04 Fmax= 3.33049e+02, atom= 3323\n",
      "Step=  621, Dmax= 2.7e-02 nm, Epot= -6.14272e+04 Fmax= 1.25677e+02, atom= 1949\n",
      "Step=  623, Dmax= 1.6e-02 nm, Epot= -6.14299e+04 Fmax= 1.41946e+02, atom= 1949\n",
      "Step=  624, Dmax= 1.9e-02 nm, Epot= -6.14319e+04 Fmax= 1.91541e+02, atom= 1949\n",
      "Step=  625, Dmax= 2.3e-02 nm, Epot= -6.14346e+04 Fmax= 1.97188e+02, atom= 1949\n",
      "Step=  627, Dmax= 1.4e-02 nm, Epot= -6.14412e+04 Fmax= 3.12574e+01, atom= 3323\n",
      "Step=  628, Dmax= 1.7e-02 nm, Epot= -6.14471e+04 Fmax= 2.47294e+02, atom= 1949\n",
      "Step=  629, Dmax= 2.0e-02 nm, Epot= -6.14568e+04 Fmax= 9.19825e+01, atom= 1949\n",
      "Step=  631, Dmax= 1.2e-02 nm, Epot= -6.14598e+04 Fmax= 1.09206e+02, atom= 1949\n",
      "Step=  632, Dmax= 1.4e-02 nm, Epot= -6.14627e+04 Fmax= 1.36560e+02, atom= 1949\n",
      "Step=  633, Dmax= 1.7e-02 nm, Epot= -6.14654e+04 Fmax= 1.53138e+02, atom= 1949\n",
      "Step=  634, Dmax= 2.1e-02 nm, Epot= -6.14674e+04 Fmax= 2.01566e+02, atom= 1949\n",
      "Step=  635, Dmax= 2.5e-02 nm, Epot= -6.14699e+04 Fmax= 2.13372e+02, atom= 1949\n",
      "Step=  637, Dmax= 1.5e-02 nm, Epot= -6.14770e+04 Fmax= 3.05146e+01, atom= 3323\n",
      "Step=  638, Dmax= 1.8e-02 nm, Epot= -6.14823e+04 Fmax= 2.71011e+02, atom= 1949\n",
      "Step=  639, Dmax= 2.1e-02 nm, Epot= -6.14939e+04 Fmax= 9.39666e+01, atom= 1949\n",
      "Step=  641, Dmax= 1.3e-02 nm, Epot= -6.14968e+04 Fmax= 1.21082e+02, atom= 1949\n",
      "Step=  642, Dmax= 1.5e-02 nm, Epot= -6.14997e+04 Fmax= 1.42449e+02, atom= 1949\n",
      "Step=  643, Dmax= 1.8e-02 nm, Epot= -6.15021e+04 Fmax= 1.67905e+02, atom= 1949\n",
      "Step=  644, Dmax= 2.2e-02 nm, Epot= -6.15040e+04 Fmax= 2.12542e+02, atom= 1949\n",
      "Step=  645, Dmax= 2.7e-02 nm, Epot= -6.15060e+04 Fmax= 2.31949e+02, atom= 1949\n",
      "Step=  647, Dmax= 1.6e-02 nm, Epot= -6.15144e+04 Fmax= 3.02890e+01, atom= 3323\n",
      "Step=  648, Dmax= 1.9e-02 nm, Epot= -6.15187e+04 Fmax= 2.87664e+02, atom= 1949\n",
      "Step=  649, Dmax= 2.3e-02 nm, Epot= -6.15322e+04 Fmax= 1.07222e+02, atom= 1949\n",
      "Step=  651, Dmax= 1.4e-02 nm, Epot= -6.15352e+04 Fmax= 1.23671e+02, atom= 1949\n",
      "Step=  652, Dmax= 1.7e-02 nm, Epot= -6.15376e+04 Fmax= 1.60224e+02, atom= 1949\n",
      "Step=  653, Dmax= 2.0e-02 nm, Epot= -6.15403e+04 Fmax= 1.73212e+02, atom= 1949\n",
      "Step=  654, Dmax= 2.4e-02 nm, Epot= -6.15413e+04 Fmax= 2.36454e+02, atom= 1949\n",
      "Step=  655, Dmax= 2.9e-02 nm, Epot= -6.15439e+04 Fmax= 2.40930e+02, atom= 1949\n",
      "Step=  657, Dmax= 1.7e-02 nm, Epot= -6.15530e+04 Fmax= 3.99922e+01, atom= 3323\n",
      "Step=  659, Dmax= 1.0e-02 nm, Epot= -6.15576e+04 Fmax= 1.33768e+02, atom= 1949\n",
      "Step=  660, Dmax= 1.2e-02 nm, Epot= -6.15620e+04 Fmax= 7.56548e+01, atom= 1949\n",
      "Step=  661, Dmax= 1.5e-02 nm, Epot= -6.15640e+04 Fmax= 1.71268e+02, atom= 1949\n",
      "Step=  662, Dmax= 1.8e-02 nm, Epot= -6.15687e+04 Fmax= 1.29578e+02, atom= 1949\n",
      "Step=  664, Dmax= 1.1e-02 nm, Epot= -6.15731e+04 Fmax= 5.24324e+01, atom= 1949\n",
      "Step=  665, Dmax= 1.3e-02 nm, Epot= -6.15767e+04 Fmax= 1.67527e+02, atom= 1949\n",
      "Step=  666, Dmax= 1.5e-02 nm, Epot= -6.15815e+04 Fmax= 9.30733e+01, atom= 1949\n",
      "Step=  667, Dmax= 1.8e-02 nm, Epot= -6.15824e+04 Fmax= 2.25481e+02, atom= 1949\n",
      "Step=  668, Dmax= 2.2e-02 nm, Epot= -6.15882e+04 Fmax= 1.47792e+02, atom= 1949\n",
      "Step=  670, Dmax= 1.3e-02 nm, Epot= -6.15926e+04 Fmax= 7.13658e+01, atom= 1949\n",
      "Step=  671, Dmax= 1.6e-02 nm, Epot= -6.15947e+04 Fmax= 1.92535e+02, atom= 1949\n",
      "Step=  672, Dmax= 1.9e-02 nm, Epot= -6.16001e+04 Fmax= 1.28400e+02, atom= 1949\n",
      "Step=  674, Dmax= 1.1e-02 nm, Epot= -6.16041e+04 Fmax= 6.58039e+01, atom= 1949\n",
      "Step=  675, Dmax= 1.4e-02 nm, Epot= -6.16072e+04 Fmax= 1.69507e+02, atom= 1949\n",
      "Step=  676, Dmax= 1.7e-02 nm, Epot= -6.16117e+04 Fmax= 1.09017e+02, atom= 1949\n",
      "Step=  677, Dmax= 2.0e-02 nm, Epot= -6.16123e+04 Fmax= 2.32233e+02, atom= 1949\n",
      "Step=  678, Dmax= 2.4e-02 nm, Epot= -6.16177e+04 Fmax= 1.67062e+02, atom= 1949\n",
      "Step=  680, Dmax= 1.4e-02 nm, Epot= -6.16228e+04 Fmax= 6.73887e+01, atom= 1949\n",
      "Step=  681, Dmax= 1.7e-02 nm, Epot= -6.16243e+04 Fmax= 2.15799e+02, atom= 1949\n",
      "Step=  682, Dmax= 2.1e-02 nm, Epot= -6.16309e+04 Fmax= 1.28582e+02, atom= 1949\n",
      "Step=  684, Dmax= 1.2e-02 nm, Epot= -6.16349e+04 Fmax= 7.97385e+01, atom= 1949\n",
      "Step=  685, Dmax= 1.5e-02 nm, Epot= -6.16372e+04 Fmax= 1.72885e+02, atom= 1949\n",
      "Step=  686, Dmax= 1.8e-02 nm, Epot= -6.16416e+04 Fmax= 1.25784e+02, atom= 1949\n",
      "Step=  687, Dmax= 2.1e-02 nm, Epot= -6.16417e+04 Fmax= 2.40575e+02, atom= 1949\n",
      "Step=  688, Dmax= 2.6e-02 nm, Epot= -6.16469e+04 Fmax= 1.87556e+02, atom= 1949\n",
      "Step=  690, Dmax= 1.5e-02 nm, Epot= -6.16529e+04 Fmax= 6.60799e+01, atom= 3323\n",
      "Step=  691, Dmax= 1.8e-02 nm, Epot= -6.16537e+04 Fmax= 2.40106e+02, atom= 3323\n",
      "Step=  692, Dmax= 2.2e-02 nm, Epot= -6.16616e+04 Fmax= 1.29555e+02, atom= 3323\n",
      "Step=  694, Dmax= 1.3e-02 nm, Epot= -6.16654e+04 Fmax= 9.36283e+01, atom= 3323\n",
      "Step=  695, Dmax= 1.6e-02 nm, Epot= -6.16674e+04 Fmax= 1.74793e+02, atom= 3323\n",
      "Step=  696, Dmax= 1.9e-02 nm, Epot= -6.16715e+04 Fmax= 1.46095e+02, atom= 3323\n",
      "Step=  698, Dmax= 1.1e-02 nm, Epot= -6.16762e+04 Fmax= 4.50594e+01, atom= 3323\n",
      "Step=  699, Dmax= 1.4e-02 nm, Epot= -6.16805e+04 Fmax= 1.84908e+02, atom= 3323\n",
      "Step=  700, Dmax= 1.6e-02 nm, Epot= -6.16862e+04 Fmax= 9.14170e+01, atom= 3323\n",
      "Step=  702, Dmax= 9.9e-03 nm, Epot= -6.16895e+04 Fmax= 7.54193e+01, atom= 3323\n",
      "Step=  703, Dmax= 1.2e-02 nm, Epot= -6.16926e+04 Fmax= 1.24684e+02, atom= 3323\n",
      "Step=  704, Dmax= 1.4e-02 nm, Epot= -6.16961e+04 Fmax= 1.14940e+02, atom= 3323\n",
      "Step=  705, Dmax= 1.7e-02 nm, Epot= -6.16980e+04 Fmax= 1.74170e+02, atom= 3323\n",
      "Step=  706, Dmax= 2.1e-02 nm, Epot= -6.17014e+04 Fmax= 1.70701e+02, atom= 3323\n",
      "Step=  707, Dmax= 2.5e-02 nm, Epot= -6.17016e+04 Fmax= 2.46551e+02, atom= 3323\n",
      "Step=  708, Dmax= 3.0e-02 nm, Epot= -6.17043e+04 Fmax= 2.49177e+02, atom= 3323\n",
      "Step=  710, Dmax= 1.8e-02 nm, Epot= -6.17140e+04 Fmax= 4.56564e+01, atom= 3323\n",
      "Step=  711, Dmax= 2.1e-02 nm, Epot= -6.17147e+04 Fmax= 3.10156e+02, atom= 3323\n",
      "Step=  712, Dmax= 2.6e-02 nm, Epot= -6.17275e+04 Fmax= 1.18057e+02, atom= 3323\n",
      "Step=  714, Dmax= 1.5e-02 nm, Epot= -6.17303e+04 Fmax= 1.40059e+02, atom= 3323\n",
      "Step=  715, Dmax= 1.8e-02 nm, Epot= -6.17327e+04 Fmax= 1.69299e+02, atom= 3323\n",
      "Step=  716, Dmax= 2.2e-02 nm, Epot= -6.17346e+04 Fmax= 2.00894e+02, atom= 3323\n",
      "Step=  717, Dmax= 2.6e-02 nm, Epot= -6.17358e+04 Fmax= 2.46036e+02, atom= 3323\n",
      "Step=  718, Dmax= 3.2e-02 nm, Epot= -6.17362e+04 Fmax= 2.85767e+02, atom= 3323\n",
      "Step=  720, Dmax= 1.9e-02 nm, Epot= -6.17488e+04 Fmax= 3.10433e+01, atom= 3323\n",
      "Step=  721, Dmax= 2.3e-02 nm, Epot= -6.17512e+04 Fmax= 3.54161e+02, atom= 3323\n",
      "Step=  722, Dmax= 2.7e-02 nm, Epot= -6.17691e+04 Fmax= 1.10459e+02, atom= 3323\n",
      "Step=  724, Dmax= 1.6e-02 nm, Epot= -6.17708e+04 Fmax= 1.67762e+02, atom= 3323\n",
      "Step=  725, Dmax= 2.0e-02 nm, Epot= -6.17742e+04 Fmax= 1.65501e+02, atom= 3323\n",
      "Step=  727, Dmax= 1.2e-02 nm, Epot= -6.17800e+04 Fmax= 3.57628e+01, atom= 3323\n",
      "Step=  728, Dmax= 1.4e-02 nm, Epot= -6.17848e+04 Fmax= 2.05701e+02, atom= 3323\n",
      "Step=  729, Dmax= 1.7e-02 nm, Epot= -6.17919e+04 Fmax= 8.54245e+01, atom= 3323\n",
      "Step=  731, Dmax= 1.0e-02 nm, Epot= -6.17950e+04 Fmax= 8.67985e+01, atom= 3323\n",
      "Step=  732, Dmax= 1.2e-02 nm, Epot= -6.17978e+04 Fmax= 1.21109e+02, atom= 3323\n",
      "Step=  733, Dmax= 1.5e-02 nm, Epot= -6.18008e+04 Fmax= 1.27346e+02, atom= 3323\n",
      "Step=  734, Dmax= 1.8e-02 nm, Epot= -6.18025e+04 Fmax= 1.70965e+02, atom= 3323\n",
      "Step=  735, Dmax= 2.1e-02 nm, Epot= -6.18049e+04 Fmax= 1.87542e+02, atom= 3323\n",
      "Step=  736, Dmax= 2.5e-02 nm, Epot= -6.18051e+04 Fmax= 2.40863e+02, atom= 3323\n",
      "Step=  737, Dmax= 3.1e-02 nm, Epot= -6.18060e+04 Fmax= 2.76327e+02, atom= 3323\n",
      "Step=  739, Dmax= 1.8e-02 nm, Epot= -6.18181e+04 Fmax= 3.75260e+01, atom= 3323\n",
      "Step=  741, Dmax= 1.1e-02 nm, Epot= -6.18229e+04 Fmax= 1.43857e+02, atom= 3323\n",
      "Step=  742, Dmax= 1.3e-02 nm, Epot= -6.18272e+04 Fmax= 8.13268e+01, atom= 3323\n",
      "Step=  743, Dmax= 1.6e-02 nm, Epot= -6.18282e+04 Fmax= 1.86414e+02, atom= 3323\n",
      "Step=  744, Dmax= 1.9e-02 nm, Epot= -6.18330e+04 Fmax= 1.36189e+02, atom= 3323\n",
      "Step=  746, Dmax= 1.1e-02 nm, Epot= -6.18373e+04 Fmax= 5.46422e+01, atom= 3323\n",
      "Step=  747, Dmax= 1.4e-02 nm, Epot= -6.18394e+04 Fmax= 1.77559e+02, atom= 3323\n",
      "Step=  748, Dmax= 1.6e-02 nm, Epot= -6.18449e+04 Fmax= 9.81546e+01, atom= 3323\n",
      "Step=  750, Dmax= 9.9e-03 nm, Epot= -6.18481e+04 Fmax= 6.92657e+01, atom= 3323\n",
      "Step=  751, Dmax= 1.2e-02 nm, Epot= -6.18505e+04 Fmax= 1.29277e+02, atom= 3323\n",
      "Step=  752, Dmax= 1.4e-02 nm, Epot= -6.18538e+04 Fmax= 1.11387e+02, atom= 3323\n",
      "Step=  753, Dmax= 1.7e-02 nm, Epot= -6.18547e+04 Fmax= 1.76156e+02, atom= 3323\n",
      "Step=  754, Dmax= 2.0e-02 nm, Epot= -6.18577e+04 Fmax= 1.69428e+02, atom= 3323\n",
      "Step=  756, Dmax= 1.2e-02 nm, Epot= -6.18638e+04 Fmax= 3.54448e+01, atom= 3323\n",
      "Step=  757, Dmax= 1.5e-02 nm, Epot= -6.18662e+04 Fmax= 2.16367e+02, atom= 3323\n",
      "Step=  758, Dmax= 1.8e-02 nm, Epot= -6.18749e+04 Fmax= 8.04779e+01, atom= 3323\n",
      "Step=  760, Dmax= 1.1e-02 nm, Epot= -6.18775e+04 Fmax= 9.98588e+01, atom= 3323\n",
      "Step=  761, Dmax= 1.3e-02 nm, Epot= -6.18799e+04 Fmax= 1.13861e+02, atom= 3323\n",
      "Step=  762, Dmax= 1.5e-02 nm, Epot= -6.18816e+04 Fmax= 1.44921e+02, atom= 3323\n",
      "Step=  763, Dmax= 1.8e-02 nm, Epot= -6.18834e+04 Fmax= 1.63846e+02, atom= 3323\n",
      "Step=  764, Dmax= 2.2e-02 nm, Epot= -6.18835e+04 Fmax= 2.07417e+02, atom= 3323\n",
      "Step=  765, Dmax= 2.6e-02 nm, Epot= -6.18839e+04 Fmax= 2.38270e+02, atom= 3323\n",
      "Step=  767, Dmax= 1.6e-02 nm, Epot= -6.18959e+04 Fmax= 3.25907e+01, atom= 3323\n",
      "Step=  769, Dmax= 9.5e-03 nm, Epot= -6.18999e+04 Fmax= 1.23018e+02, atom= 3323\n",
      "Step=  770, Dmax= 1.1e-02 nm, Epot= -6.19041e+04 Fmax= 7.19840e+01, atom= 3323\n",
      "Step=  771, Dmax= 1.4e-02 nm, Epot= -6.19044e+04 Fmax= 1.58267e+02, atom= 3323\n",
      "Step=  772, Dmax= 1.6e-02 nm, Epot= -6.19089e+04 Fmax= 1.21307e+02, atom= 3323\n",
      "Step=  774, Dmax= 9.8e-03 nm, Epot= -6.19134e+04 Fmax= 4.35690e+01, atom= 3323\n",
      "Step=  775, Dmax= 1.2e-02 nm, Epot= -6.19146e+04 Fmax= 1.59358e+02, atom= 3323\n",
      "Step=  776, Dmax= 1.4e-02 nm, Epot= -6.19206e+04 Fmax= 7.88613e+01, atom= 3323\n",
      "Step=  778, Dmax= 8.5e-03 nm, Epot= -6.19235e+04 Fmax= 6.66403e+01, atom= 3323\n",
      "Step=  779, Dmax= 1.0e-02 nm, Epot= -6.19255e+04 Fmax= 1.04174e+02, atom= 3323\n",
      "Step=  780, Dmax= 1.2e-02 nm, Epot= -6.19282e+04 Fmax= 1.04693e+02, atom= 3323\n",
      "Step=  781, Dmax= 1.5e-02 nm, Epot= -6.19292e+04 Fmax= 1.42981e+02, atom= 3323\n",
      "Step=  782, Dmax= 1.8e-02 nm, Epot= -6.19310e+04 Fmax= 1.57064e+02, atom= 1040\n",
      "Step=  784, Dmax= 1.1e-02 nm, Epot= -6.19380e+04 Fmax= 2.27104e+01, atom= 1040\n",
      "Step=  785, Dmax= 1.3e-02 nm, Epot= -6.19430e+04 Fmax= 1.90449e+02, atom= 1040\n",
      "Step=  786, Dmax= 1.5e-02 nm, Epot= -6.19515e+04 Fmax= 6.69500e+01, atom= 1040\n",
      "Step=  788, Dmax= 9.1e-03 nm, Epot= -6.19538e+04 Fmax= 8.98881e+01, atom= 1040\n",
      "Step=  789, Dmax= 1.1e-02 nm, Epot= -6.19563e+04 Fmax= 9.69127e+01, atom= 1040\n",
      "Step=  790, Dmax= 1.3e-02 nm, Epot= -6.19578e+04 Fmax= 1.27878e+02, atom= 1040\n",
      "Step=  791, Dmax= 1.6e-02 nm, Epot= -6.19599e+04 Fmax= 1.41222e+02, atom= 1040\n",
      "Step=  792, Dmax= 1.9e-02 nm, Epot= -6.19601e+04 Fmax= 1.82178e+02, atom= 1040\n",
      "Step=  793, Dmax= 2.3e-02 nm, Epot= -6.19612e+04 Fmax= 2.05354e+02, atom= 1040\n",
      "Step=  795, Dmax= 1.4e-02 nm, Epot= -6.19711e+04 Fmax= 2.85714e+01, atom= 1040\n",
      "Step=  796, Dmax= 1.6e-02 nm, Epot= -6.19713e+04 Fmax= 2.54575e+02, atom= 1040\n",
      "Step=  797, Dmax= 2.0e-02 nm, Epot= -6.19841e+04 Fmax= 8.58721e+01, atom= 1040\n",
      "Step=  799, Dmax= 1.2e-02 nm, Epot= -6.19861e+04 Fmax= 1.15620e+02, atom= 1040\n",
      "Step=  800, Dmax= 1.4e-02 nm, Epot= -6.19883e+04 Fmax= 1.26179e+02, atom= 1040\n",
      "Step=  801, Dmax= 1.7e-02 nm, Epot= -6.19892e+04 Fmax= 1.63102e+02, atom= 1040\n",
      "Step=  802, Dmax= 2.0e-02 nm, Epot= -6.19906e+04 Fmax= 1.84593e+02, atom= 1040\n",
      "Step=  804, Dmax= 1.2e-02 nm, Epot= -6.19983e+04 Fmax= 2.27677e+01, atom= 1040\n",
      "Step=  805, Dmax= 1.5e-02 nm, Epot= -6.20034e+04 Fmax= 2.24568e+02, atom= 1040\n",
      "Step=  806, Dmax= 1.8e-02 nm, Epot= -6.20131e+04 Fmax= 7.26377e+01, atom= 1040\n",
      "Step=  808, Dmax= 1.1e-02 nm, Epot= -6.20151e+04 Fmax= 1.09182e+02, atom= 1040\n",
      "Step=  809, Dmax= 1.3e-02 nm, Epot= -6.20177e+04 Fmax= 1.06686e+02, atom= 1040\n",
      "Step=  810, Dmax= 1.5e-02 nm, Epot= -6.20186e+04 Fmax= 1.52878e+02, atom= 1040\n",
      "Step=  811, Dmax= 1.8e-02 nm, Epot= -6.20209e+04 Fmax= 1.57619e+02, atom= 1040\n",
      "Step=  813, Dmax= 1.1e-02 nm, Epot= -6.20268e+04 Fmax= 2.99193e+01, atom= 1040\n",
      "Step=  814, Dmax= 1.3e-02 nm, Epot= -6.20296e+04 Fmax= 1.94079e+02, atom= 1040\n",
      "Step=  815, Dmax= 1.6e-02 nm, Epot= -6.20371e+04 Fmax= 7.75292e+01, atom= 1040\n",
      "Step=  817, Dmax= 9.5e-03 nm, Epot= -6.20396e+04 Fmax= 8.38311e+01, atom= 1040\n",
      "Step=  818, Dmax= 1.1e-02 nm, Epot= -6.20416e+04 Fmax= 1.10206e+02, atom= 1040\n",
      "Step=  819, Dmax= 1.4e-02 nm, Epot= -6.20438e+04 Fmax= 1.21578e+02, atom= 1040\n",
      "Step=  820, Dmax= 1.6e-02 nm, Epot= -6.20449e+04 Fmax= 1.57570e+02, atom= 1040\n",
      "Step=  821, Dmax= 2.0e-02 nm, Epot= -6.20464e+04 Fmax= 1.76421e+02, atom= 1040\n",
      "Step=  823, Dmax= 1.2e-02 nm, Epot= -6.20535e+04 Fmax= 3.59349e+01, atom= 1782\n",
      "Step=  824, Dmax= 1.4e-02 nm, Epot= -6.20582e+04 Fmax= 1.45222e+02, atom= 1040\n",
      "Step=  825, Dmax= 1.7e-02 nm, Epot= -6.20607e+04 Fmax= 1.46283e+02, atom= 1040\n",
      "Step=  827, Dmax= 1.0e-02 nm, Epot= -6.20664e+04 Fmax= 4.02890e+01, atom= 1782\n",
      "Step=  828, Dmax= 1.2e-02 nm, Epot= -6.20708e+04 Fmax= 1.11162e+02, atom= 1040\n",
      "Step=  829, Dmax= 1.5e-02 nm, Epot= -6.20723e+04 Fmax= 1.37422e+02, atom= 1040\n",
      "Step=  830, Dmax= 1.8e-02 nm, Epot= -6.20734e+04 Fmax= 1.63267e+02, atom= 1040\n",
      "Step=  831, Dmax= 2.1e-02 nm, Epot= -6.20738e+04 Fmax= 1.96144e+02, atom= 1040\n",
      "Step=  833, Dmax= 1.3e-02 nm, Epot= -6.20834e+04 Fmax= 4.40350e+01, atom= 1782\n",
      "Step=  834, Dmax= 1.5e-02 nm, Epot= -6.20886e+04 Fmax= 1.03352e+02, atom= 1040\n",
      "Step=  836, Dmax= 9.1e-03 nm, Epot= -6.20925e+04 Fmax= 5.41424e+01, atom= 1040\n",
      "Step=  837, Dmax= 1.1e-02 nm, Epot= -6.20932e+04 Fmax= 1.32904e+02, atom= 4937\n",
      "Step=  838, Dmax= 1.3e-02 nm, Epot= -6.20977e+04 Fmax= 9.61326e+01, atom= 4937\n",
      "Step=  840, Dmax= 7.9e-03 nm, Epot= -6.21014e+04 Fmax= 4.11376e+01, atom= 4937\n",
      "Step=  841, Dmax= 9.4e-03 nm, Epot= -6.21036e+04 Fmax= 1.17201e+02, atom= 4937\n",
      "Step=  842, Dmax= 1.1e-02 nm, Epot= -6.21076e+04 Fmax= 7.87920e+01, atom= 4937\n",
      "Step=  844, Dmax= 6.8e-03 nm, Epot= -6.21105e+04 Fmax= 3.82117e+01, atom= 4937\n",
      "Step=  845, Dmax= 8.2e-03 nm, Epot= -6.21129e+04 Fmax= 1.06706e+02, atom= 4937\n",
      "Step=  846, Dmax= 9.8e-03 nm, Epot= -6.21165e+04 Fmax= 6.35798e+01, atom= 4937\n",
      "Step=  847, Dmax= 1.2e-02 nm, Epot= -6.21170e+04 Fmax= 1.42991e+02, atom= 4937\n",
      "Step=  848, Dmax= 1.4e-02 nm, Epot= -6.21211e+04 Fmax= 1.03213e+02, atom= 4937\n",
      "Step=  850, Dmax= 8.5e-03 nm, Epot= -6.21246e+04 Fmax= 4.43484e+01, atom= 4937\n",
      "Step=  851, Dmax= 1.0e-02 nm, Epot= -6.21266e+04 Fmax= 1.25828e+02, atom= 4937\n",
      "Step=  852, Dmax= 1.2e-02 nm, Epot= -6.21303e+04 Fmax= 8.48035e+01, atom= 4937\n",
      "Step=  854, Dmax= 7.3e-03 nm, Epot= -6.21333e+04 Fmax= 4.11273e+01, atom= 4937\n",
      "Step=  855, Dmax= 8.8e-03 nm, Epot= -6.21354e+04 Fmax= 1.14631e+02, atom= 4937\n",
      "Step=  856, Dmax= 1.1e-02 nm, Epot= -6.21390e+04 Fmax= 6.88454e+01, atom= 4937\n",
      "Step=  857, Dmax= 1.3e-02 nm, Epot= -6.21392e+04 Fmax= 1.53268e+02, atom= 4937\n",
      "Step=  858, Dmax= 1.5e-02 nm, Epot= -6.21433e+04 Fmax= 1.12028e+02, atom= 4937\n",
      "Step=  860, Dmax= 9.1e-03 nm, Epot= -6.21469e+04 Fmax= 4.66405e+01, atom= 4937\n",
      "Step=  861, Dmax= 1.1e-02 nm, Epot= -6.21487e+04 Fmax= 1.36129e+02, atom= 4937\n",
      "Step=  862, Dmax= 1.3e-02 nm, Epot= -6.21526e+04 Fmax= 9.02350e+01, atom= 4937\n",
      "Step=  864, Dmax= 7.9e-03 nm, Epot= -6.21554e+04 Fmax= 4.53374e+01, atom= 4937\n",
      "Step=  865, Dmax= 9.4e-03 nm, Epot= -6.21574e+04 Fmax= 1.21818e+02, atom= 4937\n",
      "Step=  866, Dmax= 1.1e-02 nm, Epot= -6.21610e+04 Fmax= 7.56580e+01, atom= 4937\n",
      "Step=  868, Dmax= 6.8e-03 nm, Epot= -6.21636e+04 Fmax= 4.35774e+01, atom= 4937\n",
      "Step=  869, Dmax= 8.1e-03 nm, Epot= -6.21661e+04 Fmax= 9.42887e+01, atom= 4937\n",
      "Step=  870, Dmax= 9.8e-03 nm, Epot= -6.21688e+04 Fmax= 7.59747e+01, atom= 4937\n",
      "Step=  871, Dmax= 1.2e-02 nm, Epot= -6.21700e+04 Fmax= 1.25936e+02, atom= 4937\n",
      "Step=  872, Dmax= 1.4e-02 nm, Epot= -6.21728e+04 Fmax= 1.18387e+02, atom= 4937\n",
      "Step=  874, Dmax= 8.4e-03 nm, Epot= -6.21767e+04 Fmax= 2.82705e+01, atom= 4937\n",
      "Step=  875, Dmax= 1.0e-02 nm, Epot= -6.21796e+04 Fmax= 1.55920e+02, atom= 4937\n",
      "Step=  876, Dmax= 1.2e-02 nm, Epot= -6.21851e+04 Fmax= 5.99825e+01, atom= 4937\n",
      "Step=  878, Dmax= 7.3e-03 nm, Epot= -6.21875e+04 Fmax= 6.96112e+01, atom= 4937\n",
      "Step=  879, Dmax= 8.8e-03 nm, Epot= -6.21897e+04 Fmax= 8.14074e+01, atom= 4937\n",
      "Step=  880, Dmax= 1.1e-02 nm, Epot= -6.21917e+04 Fmax= 1.02919e+02, atom= 4937\n",
      "Step=  881, Dmax= 1.3e-02 nm, Epot= -6.21937e+04 Fmax= 1.16141e+02, atom= 4937\n",
      "Step=  882, Dmax= 1.5e-02 nm, Epot= -6.21949e+04 Fmax= 1.48130e+02, atom= 4937\n",
      "Step=  883, Dmax= 1.8e-02 nm, Epot= -6.21960e+04 Fmax= 1.68631e+02, atom= 4937\n",
      "Step=  884, Dmax= 2.2e-02 nm, Epot= -6.21961e+04 Fmax= 2.10300e+02, atom= 4937\n",
      "Step=  886, Dmax= 1.3e-02 nm, Epot= -6.22052e+04 Fmax= 2.65702e+01, atom= 4938\n",
      "Step=  887, Dmax= 1.6e-02 nm, Epot= -6.22084e+04 Fmax= 2.46009e+02, atom= 4938\n",
      "Step=  888, Dmax= 1.9e-02 nm, Epot= -6.22175e+04 Fmax= 9.12969e+01, atom= 4937\n",
      "Step=  890, Dmax= 1.1e-02 nm, Epot= -6.22197e+04 Fmax= 1.10043e+02, atom= 4937\n",
      "Step=  891, Dmax= 1.4e-02 nm, Epot= -6.22214e+04 Fmax= 1.25301e+02, atom= 4937\n",
      "Step=  892, Dmax= 1.6e-02 nm, Epot= -6.22226e+04 Fmax= 1.60125e+02, atom= 4937\n",
      "Step=  893, Dmax= 2.0e-02 nm, Epot= -6.22236e+04 Fmax= 1.81383e+02, atom= 4937\n",
      "Step=  895, Dmax= 1.2e-02 nm, Epot= -6.22309e+04 Fmax= 2.21315e+01, atom= 4937\n",
      "Step=  896, Dmax= 1.4e-02 nm, Epot= -6.22382e+04 Fmax= 1.89503e+02, atom= 4937\n",
      "Step=  897, Dmax= 1.7e-02 nm, Epot= -6.22443e+04 Fmax= 9.73893e+01, atom= 4937\n",
      "Step=  899, Dmax= 1.0e-02 nm, Epot= -6.22471e+04 Fmax= 8.18655e+01, atom= 4937\n",
      "Step=  900, Dmax= 1.2e-02 nm, Epot= -6.22482e+04 Fmax= 1.29203e+02, atom= 4937\n",
      "Step=  901, Dmax= 1.5e-02 nm, Epot= -6.22506e+04 Fmax= 1.25820e+02, atom= 4937\n",
      "Step=  903, Dmax= 8.7e-03 nm, Epot= -6.22551e+04 Fmax= 2.63156e+01, atom= 4937\n",
      "Step=  904, Dmax= 1.0e-02 nm, Epot= -6.22592e+04 Fmax= 1.47918e+02, atom= 938\n",
      "Step=  905, Dmax= 1.3e-02 nm, Epot= -6.22643e+04 Fmax= 7.25947e+01, atom= 938\n",
      "Step=  907, Dmax= 7.6e-03 nm, Epot= -6.22668e+04 Fmax= 6.09570e+01, atom= 938\n",
      "Step=  908, Dmax= 9.1e-03 nm, Epot= -6.22689e+04 Fmax= 9.46149e+01, atom= 938\n",
      "Step=  909, Dmax= 1.1e-02 nm, Epot= -6.22712e+04 Fmax= 9.64365e+01, atom= 938\n",
      "Step=  910, Dmax= 1.3e-02 nm, Epot= -6.22726e+04 Fmax= 1.30240e+02, atom= 938\n",
      "Step=  911, Dmax= 1.6e-02 nm, Epot= -6.22743e+04 Fmax= 1.43357e+02, atom= 938\n",
      "Step=  912, Dmax= 1.9e-02 nm, Epot= -6.22745e+04 Fmax= 1.85040e+02, atom= 938\n",
      "Step=  913, Dmax= 2.3e-02 nm, Epot= -6.22748e+04 Fmax= 2.06568e+02, atom= 938\n",
      "Step=  915, Dmax= 1.4e-02 nm, Epot= -6.22848e+04 Fmax= 2.89039e+01, atom= 939\n",
      "Step=  916, Dmax= 1.6e-02 nm, Epot= -6.22867e+04 Fmax= 2.56133e+02, atom= 938\n",
      "Step=  917, Dmax= 1.9e-02 nm, Epot= -6.22971e+04 Fmax= 9.03164e+01, atom= 938\n",
      "Step=  919, Dmax= 1.2e-02 nm, Epot= -6.22990e+04 Fmax= 1.16369e+02, atom= 938\n",
      "Step=  920, Dmax= 1.4e-02 nm, Epot= -6.23012e+04 Fmax= 1.25718e+02, atom= 938\n",
      "Step=  921, Dmax= 1.7e-02 nm, Epot= -6.23022e+04 Fmax= 1.67778e+02, atom= 938\n",
      "Step=  922, Dmax= 2.0e-02 nm, Epot= -6.23039e+04 Fmax= 1.83211e+02, atom= 938\n",
      "Step=  924, Dmax= 1.2e-02 nm, Epot= -6.23098e+04 Fmax= 2.97891e+01, atom= 938\n",
      "Step=  925, Dmax= 1.5e-02 nm, Epot= -6.23118e+04 Fmax= 2.12365e+02, atom= 938\n",
      "Step=  926, Dmax= 1.7e-02 nm, Epot= -6.23196e+04 Fmax= 9.45052e+01, atom= 938\n",
      "Step=  928, Dmax= 1.0e-02 nm, Epot= -6.23222e+04 Fmax= 8.84470e+01, atom= 9387\n",
      "Step=  929, Dmax= 1.3e-02 nm, Epot= -6.23230e+04 Fmax= 1.31686e+02, atom= 938\n",
      "Step=  930, Dmax= 1.5e-02 nm, Epot= -6.23255e+04 Fmax= 1.31326e+02, atom= 938\n",
      "Step=  932, Dmax= 9.1e-03 nm, Epot= -6.23301e+04 Fmax= 2.91377e+01, atom= 2427\n",
      "Step=  933, Dmax= 1.1e-02 nm, Epot= -6.23324e+04 Fmax= 1.65391e+02, atom= 2427\n",
      "Step=  934, Dmax= 1.3e-02 nm, Epot= -6.23384e+04 Fmax= 6.71878e+01, atom= 2427\n",
      "Step=  936, Dmax= 7.8e-03 nm, Epot= -6.23406e+04 Fmax= 6.66937e+01, atom= 4937\n",
      "Step=  937, Dmax= 9.4e-03 nm, Epot= -6.23422e+04 Fmax= 9.63323e+01, atom= 4937\n",
      "Step=  938, Dmax= 1.1e-02 nm, Epot= -6.23444e+04 Fmax= 1.01690e+02, atom= 4937\n",
      "Step=  939, Dmax= 1.4e-02 nm, Epot= -6.23452e+04 Fmax= 1.34622e+02, atom= 4937\n",
      "Step=  940, Dmax= 1.6e-02 nm, Epot= -6.23470e+04 Fmax= 1.49160e+02, atom= 4937\n",
      "Step=  942, Dmax= 9.7e-03 nm, Epot= -6.23527e+04 Fmax= 2.66976e+01, atom= 2427\n",
      "Step=  943, Dmax= 1.2e-02 nm, Epot= -6.23557e+04 Fmax= 1.79183e+02, atom= 2427\n",
      "Step=  944, Dmax= 1.4e-02 nm, Epot= -6.23619e+04 Fmax= 7.03322e+01, atom= 4937\n",
      "Step=  946, Dmax= 8.4e-03 nm, Epot= -6.23641e+04 Fmax= 7.98115e+01, atom= 4937\n",
      "Step=  947, Dmax= 1.0e-02 nm, Epot= -6.23660e+04 Fmax= 9.62597e+01, atom= 4937\n",
      "Step=  948, Dmax= 1.2e-02 nm, Epot= -6.23678e+04 Fmax= 1.17195e+02, atom= 4937\n",
      "Step=  949, Dmax= 1.5e-02 nm, Epot= -6.23691e+04 Fmax= 1.38279e+02, atom= 4937\n",
      "Step=  950, Dmax= 1.7e-02 nm, Epot= -6.23703e+04 Fmax= 1.67205e+02, atom= 4937\n",
      "Step=  951, Dmax= 2.1e-02 nm, Epot= -6.23704e+04 Fmax= 2.01543e+02, atom= 4937\n",
      "Step=  952, Dmax= 2.5e-02 nm, Epot= -6.23709e+04 Fmax= 2.35760e+02, atom= 4937\n",
      "Step=  954, Dmax= 1.5e-02 nm, Epot= -6.23809e+04 Fmax= 4.28066e+01, atom= 4938\n",
      "Step=  956, Dmax= 9.0e-03 nm, Epot= -6.23838e+04 Fmax= 1.01697e+02, atom= 4232\n",
      "Step=  957, Dmax= 1.1e-02 nm, Epot= -6.23862e+04 Fmax= 8.75414e+01, atom= 4937\n",
      "Step=  958, Dmax= 1.3e-02 nm, Epot= -6.23872e+04 Fmax= 1.43666e+02, atom= 4937\n",
      "Step=  959, Dmax= 1.6e-02 nm, Epot= -6.23897e+04 Fmax= 1.32980e+02, atom= 4937\n",
      "Step=  961, Dmax= 9.4e-03 nm, Epot= -6.23936e+04 Fmax= 3.15960e+01, atom= 4937\n",
      "Step=  962, Dmax= 1.1e-02 nm, Epot= -6.23977e+04 Fmax= 1.50721e+02, atom= 4937\n",
      "Step=  963, Dmax= 1.3e-02 nm, Epot= -6.24016e+04 Fmax= 8.27897e+01, atom= 4937\n",
      "Step=  965, Dmax= 8.1e-03 nm, Epot= -6.24039e+04 Fmax= 5.95661e+01, atom= 4937\n",
      "Step=  966, Dmax= 9.7e-03 nm, Epot= -6.24059e+04 Fmax= 1.11909e+02, atom= 4937\n",
      "Step=  967, Dmax= 1.2e-02 nm, Epot= -6.24085e+04 Fmax= 9.38756e+01, atom= 4937\n",
      "Step=  968, Dmax= 1.4e-02 nm, Epot= -6.24096e+04 Fmax= 1.52476e+02, atom= 4937\n",
      "Step=  969, Dmax= 1.7e-02 nm, Epot= -6.24120e+04 Fmax= 1.45137e+02, atom= 4937\n",
      "Step=  970, Dmax= 2.0e-02 nm, Epot= -6.24121e+04 Fmax= 2.07900e+02, atom= 4937\n",
      "Step=  971, Dmax= 2.4e-02 nm, Epot= -6.24135e+04 Fmax= 2.21125e+02, atom= 4937\n",
      "Step=  973, Dmax= 1.5e-02 nm, Epot= -6.24210e+04 Fmax= 3.03283e+01, atom= 4937\n",
      "Step=  974, Dmax= 1.7e-02 nm, Epot= -6.24262e+04 Fmax= 2.34137e+02, atom= 4937\n",
      "Step=  975, Dmax= 2.1e-02 nm, Epot= -6.24323e+04 Fmax= 1.23070e+02, atom= 4937\n",
      "Step=  977, Dmax= 1.3e-02 nm, Epot= -6.24349e+04 Fmax= 1.03752e+02, atom= 4937\n",
      "Step=  978, Dmax= 1.5e-02 nm, Epot= -6.24363e+04 Fmax= 1.55823e+02, atom= 4937\n",
      "Step=  979, Dmax= 1.8e-02 nm, Epot= -6.24382e+04 Fmax= 1.64005e+02, atom= 4937\n",
      "Step=  980, Dmax= 2.2e-02 nm, Epot= -6.24387e+04 Fmax= 2.12617e+02, atom= 4937\n",
      "Step=  981, Dmax= 2.6e-02 nm, Epot= -6.24391e+04 Fmax= 2.46961e+02, atom= 4937\n",
      "Step=  982, Dmax= 3.1e-02 nm, Epot= -6.24392e+04 Fmax= 2.92519e+02, atom= 4937\n",
      "Step=  984, Dmax= 1.9e-02 nm, Epot= -6.24498e+04 Fmax= 5.74096e+01, atom= 4938\n",
      "Step=  986, Dmax= 1.1e-02 nm, Epot= -6.24524e+04 Fmax= 1.25219e+02, atom= 4232\n",
      "Step=  987, Dmax= 1.3e-02 nm, Epot= -6.24548e+04 Fmax= 1.09413e+02, atom= 4232\n",
      "Step=  988, Dmax= 1.6e-02 nm, Epot= -6.24557e+04 Fmax= 1.79087e+02, atom= 4232\n",
      "Step=  989, Dmax= 1.9e-02 nm, Epot= -6.24583e+04 Fmax= 1.57637e+02, atom= 4232\n",
      "Step=  991, Dmax= 1.2e-02 nm, Epot= -6.24624e+04 Fmax= 4.41992e+01, atom= 4937\n",
      "Step=  992, Dmax= 1.4e-02 nm, Epot= -6.24650e+04 Fmax= 1.84347e+02, atom= 4937\n",
      "Step=  993, Dmax= 1.7e-02 nm, Epot= -6.24693e+04 Fmax= 1.04549e+02, atom= 4937\n",
      "Step=  995, Dmax= 1.0e-02 nm, Epot= -6.24717e+04 Fmax= 7.27234e+01, atom= 4937\n",
      "Step=  996, Dmax= 1.2e-02 nm, Epot= -6.24734e+04 Fmax= 1.39498e+02, atom= 4937\n",
      "Step=  997, Dmax= 1.4e-02 nm, Epot= -6.24759e+04 Fmax= 1.17886e+02, atom= 4937\n",
      "Step=  998, Dmax= 1.7e-02 nm, Epot= -6.24766e+04 Fmax= 1.89061e+02, atom= 4232\n",
      "Step=  999, Dmax= 2.1e-02 nm, Epot= -6.24787e+04 Fmax= 1.80077e+02, atom= 4937\n",
      "Step= 1000, Dmax= 2.5e-02 nm, Epot= -6.24779e+04 Fmax= 2.64158e+02, atom= 4232\n",
      "Energy minimization reached the maximum number of steps before the forces\n",
      "reached the requested precision Fmax < 10.\n",
      "\n",
      "writing lowest energy coordinates.\n",
      "\n",
      "Back Off! I just backed up em.pdb to ./#em.pdb.1#\n",
      "\n",
      "Steepest Descents did not converge to Fmax < 10 in 1001 steps.\n",
      "Potential Energy  = -6.2478738e+04\n",
      "Maximum force     =  1.8007661e+02 on atom 4937\n",
      "Norm of force     =  5.3058659e+00\n",
      "\n",
      "GROMACS reminds you: \"The greatest shortcoming of the human race is our inability to understand the exponential function.\" (Albert Bartlett)\n",
      "\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em] energy minimized structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top'}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top'}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/em/em.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n",
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Everybody Lie Down On the Floor and Keep Calm\" (KLF)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed] All files set up for a run time of 1000 ps (dt=0.01, nsteps=100000)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 2008514542\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.125 nm, buffer size 0.025 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.100 nm, buffer size 0.000 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 3 Mb of data\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{'struct': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro',\n",
       " 'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top',\n",
       " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n",
       " 'qscript': ['./local.sh'],\n",
       " 'mainselection': None,\n",
       " 'deffnm': 'md',\n",
       " 'includes': ['/home/awsm/MDPOW/mdpow/top',\n",
       "  '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top']}"
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from mdpow.equil import OctanolSimulation\n",
    "\n",
    "oct_sim = OctanolSimulation(\n",
    "    molecule=\"BENZ\",\n",
    "    forcefield=MARTINI,\n",
    "    mdp={\n",
    "        \"energy_minimize\": str(EM_FILE.absolute()),\n",
    "        \"MD_relaxed\": str(EQ_FILE.absolute()),\n",
    "        \"MD_NPT\": str(EQ_FILE.absolute()),\n",
    "        \"MD_restrained\": str(RUN_FILE.absolute()),\n",
    "    },\n",
    "    distance=4.0,\n",
    ")\n",
    "oct_sim.topology(str(BENZENE_ITP))\n",
    "oct_sim.solvate(struct=MARTINI_BENZENE, maxwarn=1)\n",
    "oct_sim.energy_minimize(maxwarn=1)\n",
    "oct_sim.MD_relaxed(runtime=1e3, dt=0.01)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 10 to 50, rlist from 1.1 to 1.228\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the GPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "100000 steps,   1000.0 ps (continuing from step 100000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 100000, remaining wall clock time:     0 s          \n",
      "NOTE: 31 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.128        0.032      398.5\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       26.842        0.894\n",
      "\n",
      "GROMACS reminds you: \"Everybody Lie Down On the Floor and Keep Calm\" (KLF)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 45,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "r = gromacs.run.MDrunner(\n",
    "    dirname=oct_sim.dirs[\"MD_relaxed\"],\n",
    "    deffnm=\"md\",\n",
    "    c=\"md.pdb\",\n",
    "    cpi=True,\n",
    "    v=True,\n",
    ")\n",
    "r.run()  # runs mdrun in the python shell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.equil : INFO     Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.gro').\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/eq.mdp': dict_keys(['nsteps', 'dt', 'pp', 't', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 't']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 't': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt'}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -t /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_relaxed/md.cpt\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n",
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "Last frame         -1 time 1000.000   \n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"It was something to at least have a choice of nightmares\" (Joseph Conrad)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT] All files set up for a run time of 10000 ps (dt=0.02, nsteps=500000)\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -33575937\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.167 nm, buffer size 0.067 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.108 nm, buffer size 0.008 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "Reading Coordinates, Velocities and Box size from old trajectory\n",
      "\n",
      "Will read whole trajectory\n",
      "\n",
      "Using frame at t = 1000 ps\n",
      "\n",
      "Starting time for run is 0 ps\n",
      "\n",
      "This run will generate roughly 15 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 10 to 25, rlist from 1.108 to 1.223\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the GPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "500000 steps,  10000.0 ps (continuing from step 500000,  10000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 500000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.060        0.015      397.1\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      114.104        0.210\n",
      "\n",
      "GROMACS reminds you: \"Your Country Needs YOU\" (U.S. Army)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "oct_sim.MD(\n",
    "    runtime=1e4, qscript=[\"local.sh\"], dt=0.02\n",
    ")\n",
    "\n",
    "r = gromacs.run.MDrunner(\n",
    "    dirname=oct_sim.dirs[\"MD_NPT\"], deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True\n",
    ")\n",
    "r.run()  # runs mdrun in the python shell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.fep   : INFO     Found starting structure '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb' (instead of '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.gro').\n",
      "/home/awsm/MDPOW/mdpow/fep.py:596: UserWarning: Directory 'FEP/octanol' already exists --- will overwrite existing files.\n",
      "  warnings.warn(wmsg)\n",
      "mdpow.fep   : WARNING  Directory 'FEP/octanol' already exists --- will overwrite existing files.\n",
      "mdpow.fep   : INFO     Solvation free energy calculation for molecule BENZ in solvent octanol.\n",
      "mdpow.fep   : INFO     Base directory is '/home/awsm/MDPOW/doc/examples/martini'\n",
      "mdpow.fep   : INFO     Using setup directories under 'FEP/octanol': {'coulomb': 'FEP/octanol/Coulomb', 'vdw': 'FEP/octanol/VDW'}\n",
      "mdpow.fep   : INFO     Default checkpoint file is '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=0\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n",
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Microsecond Here I Come\" (P.J. Van Maaren)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=0.25\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 1989017199\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Microsecond Here I Come\" (P.J. Van Maaren)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=0.5\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1346895930\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"If everything seems under control, you're just not going fast enough.\" (Mario Andretti)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=0.75\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -478482449\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"If everything seems under control, you're just not going fast enough.\" (Mario Andretti)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing coulomb for lambda=1\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 2145386303\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"The soul? There's nothing but chemistry here\" (Breaking Bad)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "gromacs.qsub: WARNING  Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n",
      "mdpow.fep   : INFO     [coulomb] Wrote array job scripts [None]\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -67141633\n",
      "\n",
      "Generated 844 of the 356590 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"The soul? There's nothing but chemistry here\" (Breaking Bad)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.05\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1247367\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Bring Out the Gimp\" (Pulp Fiction)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.1\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -438780993\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Space May Be the Final Frontier, But It's Made in a Hollywood Basement\" (Red Hot Chili Peppers)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.2\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -806387971\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Space May Be the Final Frontier, But It's Made in a Hollywood Basement\" (Red Hot Chili Peppers)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.3\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -608984233\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Let's Unzip And Let's Unfold\" (Red Hot Chili Peppers)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.4\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -102383660\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Let's Unzip And Let's Unfold\" (Red Hot Chili Peppers)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.5\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 1946023915\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"A Pretty Village Burning Makes a Pretty Fire\" (David Sandstrom)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.6\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1091582337\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"A Pretty Village Burning Makes a Pretty Fire\" (David Sandstrom)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.65\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 989822767\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"I don't want to achieve immortality through my work... I want to achieve it through not dying!\" (Woody Allen)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.7\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -33818753\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"There are three kinds of men. The one that learns by reading. The few who learn by observation. The rest of them have to pee on the electric fence for themselves.\" (Will Rogers)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.75\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1074663713\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"There are three kinds of men. The one that learns by reading. The few who learn by observation. The rest of them have to pee on the electric fence for themselves.\" (Will Rogers)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.8\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1106905097\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Trying is the first step towards failure.\" (Homer Simpson)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.85\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -1090936833\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"Trying is the first step towards failure.\" (Homer Simpson)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.9\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 1511798142\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"All that glitters may not be gold, but at least it contains free electrons.\" (John Desmond Baernal)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=0.95\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -33820819\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"All that glitters may not be gold, but at least it contains free electrons.\" (John Desmond Baernal)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "mdpow.fep   : INFO     Preparing vdw for lambda=1\n",
      "mdpow.fep   : INFO     Setting dhdl file to edr format\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] Setting up MD...\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] input mdp  = '/home/awsm/MDPOW/doc/examples/martini/run.mdp'\n",
      "gromacs.cbook: INFO     editing mdp = '/home/awsm/MDPOW/doc/examples/martini/run.mdp': dict_keys(['nsteps', 'dt', 'pp', 'maxwarn', 'couple-intramol', 'couple_lambda0', 'couple_lambda1', 'sc_alpha', 'sc_power', 'sc_sigma', 'separate-dhdl-file', 'ref_t', 'gen_temp', 'free_energy', 'couple_moltype', 'init_lambda_state', 'fep_lambdas', 'calc_lambda_neighbors', 'include'])\n",
      "gromacs.cbook: WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']\n",
      "gromacs.setup: WARNING  Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/setup.py:635: UsageWarning: Unprocessed mdp option are interpreted as options for grompp:\n",
      "{'pp': 'processed.top', 'maxwarn': 1}\n",
      "  warnings.warn(wmsg, category=UsageWarning)\n",
      "                      :-) GROMACS - gmx grompp, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n",
      "Command line:\n",
      "  gmx grompp -f md.mdp -p /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top -c /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/MD_NPT/md.pdb -n /home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx -o md.tpr -pp processed.top -maxwarn 1\n",
      "\n",
      "Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'\n",
      "Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'\n",
      "\n",
      "NOTE 1 [file md.mdp, line 109]:\n",
      "  Old option for dhdl-print-energy given: changing \"yes\" to \"total\"\n",
      "\n",
      "\n",
      "\n",
      "NOTE 2 [file md.mdp]:\n",
      "  Setting tcoupl from 'V-rescale' to 'no'. sd handles temperature coupling\n",
      "  implicitly. See the documentation for more information on which\n",
      "  parameters affect temperature for sd.\n",
      "\n",
      "\n",
      "WARNING 1 [file md.mdp]:\n",
      "  You are generating velocities so I am assuming you are equilibrating a\n",
      "  system. You are using Parrinello-Rahman pressure coupling, but this can\n",
      "  be unstable for equilibration. If your system crashes, try equilibrating\n",
      "  first with Berendsen pressure coupling. If you are not equilibrating the\n",
      "  system, you can probably ignore this warning.\n",
      "\n",
      "\n",
      "Back Off! I just backed up processed.top to ./#processed.top.1#\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to -6356998\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Number of degrees of freedom in T-Coupling group System is 15339.00\n",
      "\n",
      "There were 2 NOTEs\n",
      "\n",
      "There was 1 WARNING\n",
      "\n",
      "Back Off! I just backed up md.tpr to ./#md.tpr.1#\n",
      "\n",
      "GROMACS reminds you: \"You can get into a habit of thought in which you enjoy making fun of all those other people who don't see things as clearly as you do. We have to guard carefully against it.\" (Carl Sagan)\n",
      "\n",
      "gromacs.qsub: INFO     Setting up queuing system script './local.sh'...\n",
      "gromacs.cbook: INFO     editing txt = '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh' (9 substitutions)\n",
      "gromacs.cbook: INFO     edited txt = './local.sh'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output mdp = 'md.mdp'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output ndx = '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output tpr = 'md.tpr'\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] output runscripts = ['./local.sh']\n",
      "gromacs.setup: INFO     [/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000] All files set up for a run time of 1000 ps (dt=0.02, nsteps=50000)\n",
      "gromacs.qsub: WARNING  Not known how to make a job array for '/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/gromacs/templates/local.sh'; skipping...\n",
      "mdpow.fep   : INFO     [vdw] Wrote array job scripts [None]\n",
      "mdpow.fep   : INFO     Saved state information to '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep'; reload later with G = Goct(filename='/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Goct.fep').\n",
      "mdpow.fep   : INFO     Finished setting up all individual simulations. Now run them...\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Setting the LD random seed to 1861188408\n",
      "\n",
      "Generated 1689 of the 357435 non-bonded parameter combinations\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'BENZ'\n",
      "\n",
      "Excluding 1 bonded neighbours molecule type 'OCO'\n",
      "\n",
      "Coupling 1 copies of molecule type 'BENZ'\n",
      "\n",
      "Velocities were taken from a Maxwell distribution at 300 K\n",
      "\n",
      "Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n",
      "\n",
      "Calculated rlist for 1x1 atom pair-list as 1.292 nm, buffer size 0.192 nm\n",
      "\n",
      "Set rlist, assuming 4x4 atom pair-list, to 1.179 nm, buffer size 0.079 nm\n",
      "\n",
      "Note that mdrun will redetermine rlist based on the actual pair-list setup\n",
      "\n",
      "This run will generate roughly 6 Mb of data\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{'top': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/top/pp_system.top',\n",
       " 'ndx': '/home/awsm/MDPOW/doc/examples/martini/Equilibrium/octanol/solvation/main.ndx',\n",
       " 'qscript': ['./local.sh'],\n",
       " 'mainselection': None,\n",
       " 'deffnm': 'md',\n",
       " 'includes': ['/home/awsm/MDPOW/mdpow/top'],\n",
       " 'maxwarn': 1,\n",
       " 'couple-intramol': 'no',\n",
       " 'couple_lambda0': 'vdw',\n",
       " 'couple_lambda1': 'none',\n",
       " 'sc_alpha': 0.5,\n",
       " 'sc_power': 1,\n",
       " 'sc_sigma': 0.3,\n",
       " 'separate-dhdl-file': 'no',\n",
       " 'ref_t': 300.0,\n",
       " 'gen_temp': 300.0,\n",
       " 'free_energy': 'yes',\n",
       " 'couple_moltype': 'BENZ',\n",
       " 'init_lambda_state': 15,\n",
       " 'fep_lambdas': array([0.  , 0.05, 0.1 , 0.2 , 0.3 , 0.4 , 0.5 , 0.6 , 0.65, 0.7 , 0.75,\n",
       "        0.8 , 0.85, 0.9 , 0.95, 1.  ]),\n",
       " 'calc_lambda_neighbors': -1}"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "goct = mdpow.fep.Goct(simulation=oct_sim, runtime=1e+3, mdp=str(RUN_FILE.absolute()))\n",
    "goct.setup(dt=0.02)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "These lambda windows take about twice as long as the water calculations on the author's desktop machine."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.177 to 1.221\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.058        0.015      398.7\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      118.985        0.202\n",
      "\n",
      "GROMACS reminds you: \"Chemistry: It tends to be a messy science.\" (Gunnar von Heijne, former chair of the Nobel Committee for chemistry)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.058        0.015      398.6\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      118.740        0.202\n",
      "\n",
      "GROMACS reminds you: \"We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation.\" (Joseph Gay-Lussac, 1808)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.063        0.016      398.7\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      109.130        0.220\n",
      "\n",
      "GROMACS reminds you: \"We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation.\" (Joseph Gay-Lussac, 1808)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.055        0.014      394.1\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      124.605        0.193\n",
      "\n",
      "GROMACS reminds you: \"...sometimes a scream is better than a thesis.\" (Ralph Waldo Emerson)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.068        0.017      398.7\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      100.751        0.238\n",
      "\n",
      "GROMACS reminds you: \"Have a Nice Day\" (R. McDonald)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 16 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.069        0.017      398.8\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       99.759        0.241\n",
      "\n",
      "GROMACS reminds you: \"I wanted to make a clever chemistry joke, but the best ones Argon.\" (39.948)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.078        0.020      399.0\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       88.427        0.271\n",
      "\n",
      "GROMACS reminds you: \"I wanted to make a clever chemistry joke, but the best ones Argon.\" (39.948)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.179 to 1.223\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.061        0.015      398.6\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      113.755        0.211\n",
      "\n",
      "GROMACS reminds you: \"Science progresses best when observations force us to alter our preconceptions.\" (Vera Rubin)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.061        0.015      398.7\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      112.992        0.212\n",
      "\n",
      "GROMACS reminds you: \"There is no place like ~\" (Anonymous)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 11 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.073        0.018      398.9\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       94.679        0.253\n",
      "\n",
      "GROMACS reminds you: \"Academia is kind of like applied Marxism. The workers really do own the means of production.\" (Niklas Blomberg)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.084        0.021      399.0\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       82.075        0.292\n",
      "\n",
      "GROMACS reminds you: \"Academia is kind of like applied Marxism. The workers really do own the means of production.\" (Niklas Blomberg)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.054        0.013      398.5\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      128.290        0.187\n",
      "\n",
      "GROMACS reminds you: \"My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)\" (Gogol Bordello)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 44 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.141        0.035      399.4\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       48.911        0.491\n",
      "\n",
      "GROMACS reminds you: \"For the first time we can now mechanically simulate the cognitive process. We can make studies in artificial intelligence. Beyond that, this mechanism can be used to assist humans in learning. As we are going to have more mature students in greater numbers as time goes on, this type of teaching will probably be increasingly important.\" (Sister Mary Kenneth Keller)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.057        0.014      398.7\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      120.860        0.199\n",
      "\n",
      "GROMACS reminds you: \"After a few talks we usually sit down to do some work... or drinking.\" (Mike Klein)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 12 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.088        0.022      396.5\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       77.863        0.308\n",
      "\n",
      "GROMACS reminds you: \"After a few talks we usually sit down to do some work... or drinking.\" (Mike Klein)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.054        0.014      398.6\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      127.768        0.188\n",
      "\n",
      "GROMACS reminds you: \"Step On the Brakes\" (2 Unlimited)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 23 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.072        0.018      398.9\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:       95.165        0.252\n",
      "\n",
      "GROMACS reminds you: \"Here's the Way It Might End\" (G. Michael)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.223\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.064        0.016      398.7\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      107.736        0.223\n",
      "\n",
      "GROMACS reminds you: \"As we all know, blinking lights means science.\" (Joss Whedon)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.059        0.015      398.6\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      116.516        0.206\n",
      "\n",
      "GROMACS reminds you: \"This is Tense !\" (Star Wars Episode I The Phantom Menace)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "NOTE: 20 % of the run time was spent in pair search,\n",
      "      you might want to increase nstlist (this has no effect on accuracy)\n",
      "\n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.067        0.017      398.8\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      103.547        0.232\n",
      "\n",
      "GROMACS reminds you: \"This is Tense !\" (Star Wars Episode I The Phantom Menace)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n",
      "gromacs.run : INFO     gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "                      :-) GROMACS - gmx mdrun, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000\n",
      "Command line:\n",
      "  gmx mdrun -deffnm md -c md.pdb -cpi -v -dhdl\n",
      "\n",
      "Reading file md.tpr, VERSION 2023.2 (single precision)\n",
      "Changing nstlist from 20 to 25, rlist from 1.178 to 1.222\n",
      "\n",
      "1 GPU selected for this run.\n",
      "Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:\n",
      "  PP:0\n",
      "PP tasks will do (non-perturbed) short-ranged interactions on the GPU\n",
      "PP task will update and constrain coordinates on the CPU\n",
      "Using 1 MPI thread\n",
      "Using 4 OpenMP threads \n",
      "\n",
      "starting mdrun 'Compound BENZ in octanol in water'\n",
      "50000 steps,   1000.0 ps (continuing from step 50000,   1000.0 ps).\n",
      "\n",
      "Writing final coordinates.\n",
      "\n",
      "Back Off! I just backed up md.pdb to ./#md.pdb.1#\n",
      "step 50000, remaining wall clock time:     0 s          \n",
      "               Core t (s)   Wall t (s)        (%)\n",
      "       Time:        0.056        0.014      392.0\n",
      "                 (ns/day)    (hour/ns)\n",
      "Performance:      119.907        0.200\n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "gromacs.run : INFO     MDrun completed ok, returncode = 0\n"
     ]
    }
   ],
   "source": [
    "for dir_ in goct.fep_dirs():\n",
    "    r = gromacs.run.MDrunner(\n",
    "        dirname=dir_, deffnm=\"md\", c=\"md.pdb\", cpi=True, v=True, dhdl=True\n",
    "    )\n",
    "    r.run()  # runs mdrun in the python shell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.fep   : INFO     [FEP/octanol] Converting EDR -> XVG.bz2\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame    200 time  800.000         mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n",
      "Last energy frame read 250 time 1000.000         \n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg\n",
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg\n",
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg\n",
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg\n",
      "\n",
      "\n",
      "Wrote 8 lambda values with 4982 samples as 2008 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Heavier-than-air flying machines are impossible.\" (Lord Kelvin, President of Royal Society, 1895.)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame     60 time  240.000         "
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.tpr, VERSION 2023.2 (single precision)\n",
      "Reading energy frame    200 time  800.000         "
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Last energy frame read 250 time 1000.000         \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO       /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr --> /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n",
      "                      :-) GROMACS - gmx energy, 2023.2 (-:\n",
      "\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/awsm/MDPOW/doc/examples/martini\n",
      "Command line:\n",
      "  gmx energy -s /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.tpr -f /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr -odh /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n",
      "\n",
      "Opened /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.edr as single precision energy file\n",
      "Reading file /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.tpr, VERSION 2023.2 (single precision)\n",
      "Last energy frame read 250 time 1000.000          \n",
      "\n",
      "GROMACS reminds you: \"Teemu [Murtola] keeps beating our code, but that's fine because he's always right.\" (Berk Hess)\n",
      "\n",
      "mdpow.fep   : INFO     Analysis stride is 1.\n",
      "mdpow.fep   : INFO     Analysis starts from frame 0.\n",
      "mdpow.fep   : INFO     Analysis stops at frame None.\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0000/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0250/md.xvg.bz2'\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg\n",
      "\n",
      "\n",
      "Wrote 19 lambda values with 4982 samples as 4769 dH data blocks to /home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0500/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/0750/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/Coulomb/1000/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0000/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0050/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0100/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0200/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0300/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0400/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0500/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0600/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0650/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0700/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0750/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0800/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0850/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0900/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/0950/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compressing dgdl file '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg' with bzip2\n",
      "mdpow.fep   : INFO     [FEP/octanol] Compression complete: '/home/awsm/MDPOW/doc/examples/martini/FEP/octanol/VDW/1000/md.xvg.bz2'\n",
      "mdpow.fep   : INFO     [FEP/octanol] Finding dgdl xvg files, reading with stride=1 permissive=False.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 0000\n",
      "\u001b[32m2023-09-04 22:41:16.809\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:16.812\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 15.84.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:16.813\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 312.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 7.9840.\n",
      "mdpow.fep   : INFO     The data are subsampled every 8 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 0250\n",
      "\u001b[32m2023-09-04 22:41:16.884\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:16.887\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 19.32.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:16.888\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 250.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 9.9640.\n",
      "mdpow.fep   : INFO     The data are subsampled every 10 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 0500\n",
      "\u001b[32m2023-09-04 22:41:16.961\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:16.963\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.68.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:16.963\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 9.4715.\n",
      "mdpow.fep   : INFO     The data are subsampled every 10 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 0750\n",
      "\u001b[32m2023-09-04 22:41:17.036\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.038\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 26.28.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.039\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 185.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 13.4649.\n",
      "mdpow.fep   : INFO     The data are subsampled every 14 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window coulomb 1000\n",
      "\u001b[32m2023-09-04 22:41:17.113\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.118\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 25.10.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.119\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 192.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 12.9740.\n",
      "mdpow.fep   : INFO     The data are subsampled every 13 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0000\n",
      "\u001b[32m2023-09-04 22:41:17.331\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.333\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.09.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.333\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 9.4715.\n",
      "mdpow.fep   : INFO     The data are subsampled every 10 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0050\n",
      "\u001b[32m2023-09-04 22:41:17.543\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.545\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 24.34.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.546\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 200.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 12.4550.\n",
      "mdpow.fep   : INFO     The data are subsampled every 13 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0100\n",
      "\u001b[32m2023-09-04 22:41:17.800\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.802\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.81.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:17.802\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.9928.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0200\n",
      "\u001b[32m2023-09-04 22:41:18.078\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.081\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 30.67.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.082\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 161.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 15.4720.\n",
      "mdpow.fep   : INFO     The data are subsampled every 16 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0300\n",
      "\u001b[32m2023-09-04 22:41:18.295\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.296\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.93.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.297\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.4728.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0400\n",
      "\u001b[32m2023-09-04 22:41:18.511\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.512\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.32.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.513\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.4728.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0500\n",
      "\u001b[32m2023-09-04 22:41:18.731\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.732\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.77.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.733\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.9928.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0600\n",
      "\u001b[32m2023-09-04 22:41:18.942\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.943\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.68.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:18.944\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.9928.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0650\n",
      "\u001b[32m2023-09-04 22:41:19.168\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:19.169\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.03.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:19.170\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.9928.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0700\n",
      "\u001b[32m2023-09-04 22:41:19.399\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:19.400\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 17.22.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:19.401\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 277.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.9928.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0750\n",
      "\u001b[32m2023-09-04 22:41:19.637\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:19.638\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.34.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:19.639\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 9.4715.\n",
      "mdpow.fep   : INFO     The data are subsampled every 10 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0800\n",
      "\u001b[32m2023-09-04 22:41:19.853\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:19.854\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.97.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:19.855\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.4728.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0850\n",
      "\u001b[32m2023-09-04 22:41:20.088\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:20.089\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.34.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:20.090\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 9.4715.\n",
      "mdpow.fep   : INFO     The data are subsampled every 10 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0900\n",
      "\u001b[32m2023-09-04 22:41:20.323\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:20.324\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.22.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:20.325\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 9.4715.\n",
      "mdpow.fep   : INFO     The data are subsampled every 10 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 0950\n",
      "\u001b[32m2023-09-04 22:41:20.541\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:20.542\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 18.59.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:20.543\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 263.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 9.4715.\n",
      "mdpow.fep   : INFO     The data are subsampled every 10 frames.\n",
      "mdpow.fep   : INFO     Performing statistical inefficiency analysis for window vdw 1000\n",
      "\u001b[32m2023-09-04 22:41:20.771\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m520\u001b[0m - \u001b[34m\u001b[1mRunning statistical inefficiency analysis.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:20.772\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m522\u001b[0m - \u001b[34m\u001b[1mStatistical inefficiency: 16.95.\u001b[0m\n",
      "\u001b[32m2023-09-04 22:41:20.775\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36malchemlyb.preprocessing.subsampling\u001b[0m:\u001b[36mstatistical_inefficiency\u001b[0m:\u001b[36m528\u001b[0m - \u001b[34m\u001b[1mNumber of uncorrelated samples: 294.\u001b[0m\n",
      "mdpow.fep   : INFO     The statistical inefficiency value is 8.4728.\n",
      "mdpow.fep   : INFO     The data are subsampled every 9 frames.\n",
      "/home/awsm/mambaforge/envs/mdpow/lib/python3.11/site-packages/pymbar/other_estimators.py:510: RuntimeWarning: invalid value encountered in sqrt\n",
      "  dDeltaF = np.sqrt(variance)\n",
      "mdpow.fep   : INFO     DeltaG0 = -(DeltaG_coul + DeltaG_vdw)\n",
      "mdpow.fep   : INFO     [BENZ] Octanol solvation free energy (coulomb) 0 (nan) kJ/mol\n",
      "mdpow.fep   : INFO     [BENZ] Octanol solvation free energy (vdw) 6.69992 (0.20) kJ/mol\n",
      "mdpow.fep   : INFO     [BENZ] Octanol solvation free energy (Gibbs) -6.69992 (nan) kJ/mol\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "-6.69992 (nan)"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "goct.convert_edr()\n",
    "goct.analyze_alchemlyb()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Results\n",
    "\n",
    "Finally, we can compare the calculated free energies of solvation, taking the difference to find the free energy of transfer and then converting to a partition coefficient."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "mdpow.fep   : INFO     [BENZ] transfer free energy water --> octanol calculation\n",
      "mdpow.fep   : INFO     The solvent is water .\n",
      "mdpow.fep   : INFO     Using already calculated free energy DeltaA\n",
      "mdpow.fep   : INFO     The solvent is octanol .\n",
      "mdpow.fep   : INFO     Using already calculated free energy DeltaA\n",
      "mdpow.fep   : INFO     [BENZ] Values at T = 300 K\n",
      "mdpow.fep   : INFO     [BENZ] Free energy of transfer water --> octanol: -13.445 (nan) kJ/mol\n",
      "mdpow.fep   : INFO     [BENZ] log P_ow: 2.341 (nan)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "log P_ow = 2.340869841742325 ± nan\n"
     ]
    }
   ],
   "source": [
    "delta_G, p_OW = mdpow.fep.pOW(gwat, goct)\n",
    "print(f\"log P_ow = {p_OW.value} ± {p_OW.error}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The actual value is $\\log P_{ow} \\approx 2.13$."
   ]
  }
 ],
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